From 3280819af380c2054074185057fae95c24192c29 Mon Sep 17 00:00:00 2001 From: Ivo Leist Date: Mon, 29 Dec 2025 14:24:23 +0100 Subject: [PATCH 1/6] Checkpoint from VS Code for cloud agent session --- omicsdm-server/pipelines/snakemake/all/README.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 omicsdm-server/pipelines/snakemake/all/README.md diff --git a/omicsdm-server/pipelines/snakemake/all/README.md b/omicsdm-server/pipelines/snakemake/all/README.md new file mode 100644 index 0000000..0966390 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/README.md @@ -0,0 +1,16 @@ +Goal: +One docker container image that is able to run the entire pipeline + +Bulk RNA-seq: + +1. DESeq2 +2. FGSEA (DESeq2 output as input) + +Single-cell RNA-seq: + +3. sc_normalisation + +Use signifcant gene sets from FGSEA as input for: + +4.a z_scoring +4.b gsva From df64b288316f34efa6d0dd74b088a0547b990090 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 29 Dec 2025 13:33:11 +0000 Subject: [PATCH 2/6] Add combined pipeline structure for all workflows Co-authored-by: IvoLeist <28399610+IvoLeist@users.noreply.github.com> --- .../pipelines/snakemake/all/.Rprofile | 1 + .../pipelines/snakemake/all/.dockerignore | 16 + .../pipelines/snakemake/all/.gitignore | 8 + .../pipelines/snakemake/all/.renvignore | 1 + .../pipelines/snakemake/all/Dockerfile | 75 + .../pipelines/snakemake/all/Snakefile | 220 ++ .../snakemake/all/config/deseq2.json | 1 + .../pipelines/snakemake/all/config/fgsea.json | 1 + .../pipelines/snakemake/all/config/gsva.json | 6 + .../all/config/sc_normalisation.json | 4 + .../snakemake/all/config/z_scoring.json | 6 + .../snakemake/all/docker-compose.yaml | 16 + .../pipelines/snakemake/all/makefile | 40 + .../pipelines/snakemake/all/renv.lock | 2519 +++++++++++++++++ .../pipelines/snakemake/all/requirements.txt | 45 + .../pipelines/snakemake/all/rules/renv.smk | 38 + .../snakemake/all/src/deseq2/deseq2.R | 1 + .../all/src/deseq2/get_data_and_preprocess.R | 1 + .../src/deseq2/get_data_and_preprocess_new.R | 1 + .../pipelines/snakemake/all/src/fgsea/fgsea.R | 1 + .../snakemake/all/src/fgsea/get_data.R | 1 + .../snakemake/all/src/fgsea/reactome2gmt.R | 1 + .../snakemake/all/src/fgsea_wrapper.R | 66 + .../snakemake/all/src/gsva/get_data.sh | 1 + .../all/src/gsva/sc_genesets_scoring_gsva.py | 1 + .../snakemake/all/src/lib/build_report.R | 1 + .../snakemake/all/src/lib/install_renv.R | 1 + .../snakemake/all/src/report/index.Rmd | 1 + .../pipelines/snakemake/all/src/report/libs.R | 1 + .../all/src/sc_normalisation/get_data.sh | 1 + .../sc_normalisation/scRNA_normalisation.py | 1 + .../snakemake/all/src/z_scoring/get_data.sh | 1 + .../src/z_scoring/sc_genesets_z_scoring.py | 1 + 33 files changed, 3079 insertions(+) create mode 100644 omicsdm-server/pipelines/snakemake/all/.Rprofile create mode 100644 omicsdm-server/pipelines/snakemake/all/.dockerignore create mode 100644 omicsdm-server/pipelines/snakemake/all/.gitignore create mode 100644 omicsdm-server/pipelines/snakemake/all/.renvignore create mode 100644 omicsdm-server/pipelines/snakemake/all/Dockerfile create mode 100644 omicsdm-server/pipelines/snakemake/all/Snakefile create mode 120000 omicsdm-server/pipelines/snakemake/all/config/deseq2.json create mode 120000 omicsdm-server/pipelines/snakemake/all/config/fgsea.json create mode 100644 omicsdm-server/pipelines/snakemake/all/config/gsva.json create mode 100644 omicsdm-server/pipelines/snakemake/all/config/sc_normalisation.json create mode 100644 omicsdm-server/pipelines/snakemake/all/config/z_scoring.json create mode 100644 omicsdm-server/pipelines/snakemake/all/docker-compose.yaml create mode 100644 omicsdm-server/pipelines/snakemake/all/makefile create mode 100644 omicsdm-server/pipelines/snakemake/all/renv.lock create mode 100644 omicsdm-server/pipelines/snakemake/all/requirements.txt create mode 100644 omicsdm-server/pipelines/snakemake/all/rules/renv.smk create mode 120000 omicsdm-server/pipelines/snakemake/all/src/deseq2/deseq2.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess_new.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/fgsea/fgsea.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/fgsea/get_data.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/fgsea/reactome2gmt.R create mode 100644 omicsdm-server/pipelines/snakemake/all/src/fgsea_wrapper.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/gsva/get_data.sh create mode 120000 omicsdm-server/pipelines/snakemake/all/src/gsva/sc_genesets_scoring_gsva.py create mode 120000 omicsdm-server/pipelines/snakemake/all/src/lib/build_report.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/lib/install_renv.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/report/index.Rmd create mode 120000 omicsdm-server/pipelines/snakemake/all/src/report/libs.R create mode 120000 omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/get_data.sh create mode 120000 omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/scRNA_normalisation.py create mode 120000 omicsdm-server/pipelines/snakemake/all/src/z_scoring/get_data.sh create mode 120000 omicsdm-server/pipelines/snakemake/all/src/z_scoring/sc_genesets_z_scoring.py diff --git a/omicsdm-server/pipelines/snakemake/all/.Rprofile b/omicsdm-server/pipelines/snakemake/all/.Rprofile new file mode 100644 index 0000000..81b960f --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/.Rprofile @@ -0,0 +1 @@ +source("renv/activate.R") diff --git a/omicsdm-server/pipelines/snakemake/all/.dockerignore b/omicsdm-server/pipelines/snakemake/all/.dockerignore new file mode 100644 index 0000000..19be7f6 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/.dockerignore @@ -0,0 +1,16 @@ +.Rproj.user +.snakemake +log +out +renv +.dockerignore +.gitignore +.Rhistory +.Rprofile +*.Rproj +docker-compose.yaml +Dockerfile +README.md +renv_bk +Snakefile +venv diff --git a/omicsdm-server/pipelines/snakemake/all/.gitignore b/omicsdm-server/pipelines/snakemake/all/.gitignore new file mode 100644 index 0000000..6685ab9 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/.gitignore @@ -0,0 +1,8 @@ +.snakemake +log +out +renv +venv +*.Rproj +.Rproj.user +.Rhistory diff --git a/omicsdm-server/pipelines/snakemake/all/.renvignore b/omicsdm-server/pipelines/snakemake/all/.renvignore new file mode 100644 index 0000000..5ceb386 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/.renvignore @@ -0,0 +1 @@ +venv diff --git a/omicsdm-server/pipelines/snakemake/all/Dockerfile b/omicsdm-server/pipelines/snakemake/all/Dockerfile new file mode 100644 index 0000000..3794f46 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/Dockerfile @@ -0,0 +1,75 @@ +FROM rocker/r-ver:4.4.0 + +# Install system dependencies for both R and Python packages +RUN apt-get update && apt-get install -y \ + curl \ + jq \ + python3 \ + python3.10-venv \ + python3-pip \ + libxml2 \ + pandoc \ + git \ + libfontconfig1-dev \ + libfreetype6-dev \ + libicu-dev \ + libglpk-dev \ + libpng-dev \ + libxml2-dev \ + libfribidi-dev \ + libharfbuzz-dev \ + zlib1g-dev \ + libbz2-dev \ + liblzma-dev \ + libzstd-dev \ + libdeflate-dev \ + libpcre2-dev \ + libreadline-dev \ + libcurl4-openssl-dev \ + libglpk-dev \ + libmagick++-dev \ + libssl-dev \ + unzip + +# Set BLAS and LAPACK to libblas +RUN ARCH=$(uname -m) && \ + update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/blas/libblas.so.3" && \ + update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/lapack/liblapack.so.3" + +# Install Snakemake and Python packages +RUN python3 -m venv /home/venv +RUN /home/venv/bin/pip install snakemake +RUN /home/venv/bin/pip install pulp==2.7.0 + +# Install awscli +RUN curl https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip -o awscliv2.zip && \ + unzip awscliv2.zip && \ + ./aws/install && \ + rm -rf awscliv2.zip aws + +# Install Python dependencies +COPY requirements.txt /tmp/requirements.txt +RUN /home/venv/bin/pip install --no-cache-dir -r /tmp/requirements.txt + +# Install R package manager (pak) and renv +RUN R -e 'install.packages("pak",repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s",.Platform$pkgType,R.Version()$os,R.Version()$arch));' +RUN R -e "pak::pkg_install('renv')" + +# Set up working directory +WORKDIR /home + +# Copy project files +COPY .renvignore . +COPY renv.lock . + +# Install R dependencies +ENV RENV_CONFIG_PAK_ENABLED=TRUE +RUN R -e "renv::restore()" + +# Copy the rest of the project +COPY . . + +# Create necessary directories +RUN mkdir -p in out log + +CMD [ "sh" ] diff --git a/omicsdm-server/pipelines/snakemake/all/Snakefile b/omicsdm-server/pipelines/snakemake/all/Snakefile new file mode 100644 index 0000000..87a5b13 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/Snakefile @@ -0,0 +1,220 @@ +PROJ_NAME = "all" + +# --- Variable Declarations ---- # +runR = "Rscript --no-save --no-restore --verbose" +runPython = "venv/bin/python3" +logAll = "2>&1" + + +rule all: + input: + report_html=f"out/_main.html", + + +rule report: + input: + # Outputs from all pipelines + deseq2_results="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", + fgsea_results=directory("out/results/fgsea"), + sc_norm_results="out/results/sc_normalisation/normalised.h5ad", + z_scoring_results="out/results/z_scoring/z-scored.h5ad", + gsva_results="out/results/gsva/gsva-scored.h5ad", + rmd="src/report/index.Rmd", + output: + html="out/_main.html", + book=directory("out/_book"), + log: + "log/report.log", + shell: + """ + cp {input.rmd} out/. + {runR} src/lib/build_report.R | tee {log} + """ + + +# --- Bulk RNA-seq Pipeline --- # + +# 1. DESeq2 Analysis +rule deseq2_analysis: + input: + rds_obj1="out/rds/deseq2_obj1.rds", + rds_obj2="out/rds/deseq2_obj2.rds", + config="config/deseq2.json", + output: + out3="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", + out5="out/results/deseq2/sessionInfo/sessionInfo.txt", + log: + "log/deseq2_analysis.log", + shell: + """ + mkdir -p out/results/deseq2/sessionInfo + {runR} src/deseq2/deseq2.R | tee {log} + """ + + +rule deseq2_get_data: + input: + config="config/deseq2.json", + output: + rds_obj1="out/rds/deseq2_obj1.rds", + rds_obj2="out/rds/deseq2_obj2.rds", + log: + "log/deseq2_get_data.log", + shell: + """ + mkdir -p out/rds + {runR} src/deseq2/get_data_and_preprocess.R {input.config} | tee {log} + """ + + +# 2. FGSEA Analysis (depends on DESeq2 output) +rule fgsea_analysis: + input: + in1="in/fgsea/results.tar.gz", + in2="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", + config="config/fgsea.json", + # Ensure DESeq2 completes first + deseq2_done="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", + output: + out7="out/results/fgsea/sessionInfo/sessionInfo.txt", + out8="out/results/fgsea/sessionInfo/platform.rds", + out9="out/results/fgsea/sessionInfo/packages.rds", + significant_genesets="out/results/fgsea/significant_genesets.gmt", + log: + "log/fgsea_analysis.log", + shell: + """ + mkdir -p out/results/fgsea/sessionInfo + {runR} src/fgsea_wrapper.R | tee {log} + """ + + +rule fgsea_get_data: + input: + config="config/fgsea.json", + output: + out1="in/fgsea/results.tar.gz", + out4="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", + log: + "log/fgsea_get_data.log", + shell: + """ + mkdir -p in/fgsea out/tmp + {runR} src/fgsea/get_data.R {input.config} | tee {log} + """ + + +# --- Single-cell RNA-seq Pipeline --- # + +# 3. Single-cell Normalisation +rule sc_normalisation: + input: + in1="in/sc_normalisation/data.h5ad", + config="config/sc_normalisation.json", + output: + out1="out/results/sc_normalisation/normalised.h5ad", + log: + "log/sc_normalisation.log", + shell: + """ + mkdir -p out/results/sc_normalisation + {runPython} src/sc_normalisation/scRNA_normalisation.py \ + --path {input.in1} | tee {log} + cp normalised.h5ad {output.out1} + """ + + +rule sc_normalisation_get_data: + input: + config="config/sc_normalisation.json", + output: + out1="in/sc_normalisation/data.h5ad", + log: + "log/sc_normalisation_get_data.log", + shell: + """ + mkdir -p in/sc_normalisation + bash src/sc_normalisation/get_data.sh | tee {log} + """ + + +# --- Gene Set Scoring Pipelines (depend on FGSEA significant gene sets) --- # + +# 4.a Z-scoring +rule z_scoring: + input: + original_h5ad="in/z_scoring/original.h5ad", + normalised_h5ad="out/results/sc_normalisation/normalised.h5ad", + gene_sets="out/results/fgsea/significant_genesets.gmt", + config="config/z_scoring.json", + output: + out1="out/results/z_scoring/z_scores.tsv", + out2="out/results/z_scoring/z-scored.h5ad", + log: + "log/z_scoring.log", + shell: + """ + mkdir -p out/results/z_scoring + {runPython} src/z_scoring/sc_genesets_z_scoring.py \ + --original_h5ad {input.original_h5ad} \ + --normalised_h5ad {input.normalised_h5ad} \ + --gene_sets {input.gene_sets} | tee {log} + cp z_scores.tsv {output.out1} + cp z-scored.h5ad {output.out2} + """ + + +rule z_scoring_get_data: + input: + config="config/z_scoring.json", + output: + out1="in/z_scoring/original.h5ad", + log: + "log/z_scoring_get_data.log", + shell: + """ + mkdir -p in/z_scoring + bash src/z_scoring/get_data.sh | tee {log} + """ + + +# 4.b GSVA +rule gsva: + input: + original_h5ad="in/gsva/original.h5ad", + normalised_h5ad="out/results/sc_normalisation/normalised.h5ad", + gene_sets="out/results/fgsea/significant_genesets.gmt", + config="config/gsva.json", + output: + out1="out/results/gsva/gsva_scores.tsv", + out2="out/results/gsva/gsva-scored.h5ad", + log: + "log/gsva.log", + shell: + """ + mkdir -p out/results/gsva + {runPython} src/gsva/sc_genesets_scoring_gsva.py \ + --original_h5ad {input.original_h5ad} \ + --normalised_h5ad {input.normalised_h5ad} \ + --gene_sets {input.gene_sets} | tee {log} + cp gsva_scores.tsv {output.out1} + cp gsva-scored.h5ad {output.out2} + """ + + +rule gsva_get_data: + input: + config="config/gsva.json", + output: + out1="in/gsva/original.h5ad", + log: + "log/gsva_get_data.log", + shell: + """ + mkdir -p in/gsva + bash src/gsva/get_data.sh | tee {log} + """ + + +# 2. Other rules +include: "rules/renv.smk" diff --git a/omicsdm-server/pipelines/snakemake/all/config/deseq2.json b/omicsdm-server/pipelines/snakemake/all/config/deseq2.json new file mode 120000 index 0000000..8c6b234 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/config/deseq2.json @@ -0,0 +1 @@ +../../../deseq2/config/deseq2.json \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/config/fgsea.json b/omicsdm-server/pipelines/snakemake/all/config/fgsea.json new file mode 120000 index 0000000..9599773 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/config/fgsea.json @@ -0,0 +1 @@ +../../../fgsea/config/fgsea.json \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/config/gsva.json b/omicsdm-server/pipelines/snakemake/all/config/gsva.json new file mode 100644 index 0000000..aa301e6 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/config/gsva.json @@ -0,0 +1,6 @@ +{ + "original_h5ad": "in/gsva/original.h5ad", + "normalised_h5ad": "out/results/sc_normalisation/normalised.h5ad", + "gene_sets": "out/results/fgsea/significant_genesets.gmt", + "output_path": "out/results/gsva" +} diff --git a/omicsdm-server/pipelines/snakemake/all/config/sc_normalisation.json b/omicsdm-server/pipelines/snakemake/all/config/sc_normalisation.json new file mode 100644 index 0000000..a294e6e --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/config/sc_normalisation.json @@ -0,0 +1,4 @@ +{ + "data_path": "in/sc_normalisation/data.h5ad", + "output_path": "out/results/sc_normalisation/normalised.h5ad" +} diff --git a/omicsdm-server/pipelines/snakemake/all/config/z_scoring.json b/omicsdm-server/pipelines/snakemake/all/config/z_scoring.json new file mode 100644 index 0000000..463a7fd --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/config/z_scoring.json @@ -0,0 +1,6 @@ +{ + "original_h5ad": "in/z_scoring/original.h5ad", + "normalised_h5ad": "out/results/sc_normalisation/normalised.h5ad", + "gene_sets": "out/results/fgsea/significant_genesets.gmt", + "output_path": "out/results/z_scoring" +} diff --git a/omicsdm-server/pipelines/snakemake/all/docker-compose.yaml b/omicsdm-server/pipelines/snakemake/all/docker-compose.yaml new file mode 100644 index 0000000..df8aa0e --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/docker-compose.yaml @@ -0,0 +1,16 @@ +version: '3.7' + +services: + all-pipeline: + build: + context: . + environment: + - CURL_CA_BUNDLE=/home/certs/vm2rootCA.pem + volumes: + - ./certs:/home/certs + - ./docker-out:/home/out + - ./docker-out/log:/home/log + tty: true + command: bash + extra_hosts: + - "panoptes.vm2.dev:host-ip" diff --git a/omicsdm-server/pipelines/snakemake/all/makefile b/omicsdm-server/pipelines/snakemake/all/makefile new file mode 100644 index 0000000..002cb63 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/makefile @@ -0,0 +1,40 @@ +.PHONY: build run test clean help + +IMAGE_NAME = omicsdm-all-pipeline +IMAGE_TAG = latest + +help: + @echo "Available targets:" + @echo " build - Build the Docker image" + @echo " run - Run the pipeline in Docker" + @echo " test - Run pipeline tests" + @echo " clean - Clean output directories" + @echo " shell - Open shell in Docker container" + +build: + docker build -t $(IMAGE_NAME):$(IMAGE_TAG) . + +run: + docker run --rm \ + -v $(PWD)/Snakefile:/home/Snakefile:ro \ + -v $(PWD)/src:/home/src:ro \ + -v $(PWD)/config:/home/config:ro \ + -v $(PWD)/docker-out:/home/out \ + --add-host minio.omicsdm.cnag.dev:172.16.10.112 \ + -it $(IMAGE_NAME):$(IMAGE_TAG) /home/venv/bin/snakemake -F + +shell: + docker run --rm \ + -v $(PWD)/Snakefile:/home/Snakefile:ro \ + -v $(PWD)/src:/home/src:ro \ + -v $(PWD)/config:/home/config:ro \ + -v $(PWD)/docker-out:/home/out \ + --add-host minio.omicsdm.cnag.dev:172.16.10.112 \ + -it $(IMAGE_NAME):$(IMAGE_TAG) bash + +clean: + rm -rf docker-out out log .snakemake + +test: + @echo "Running 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+h5py==3.14.0 +Jinja2==3.1.6 +joblib==1.5.1 +kiwisolver==1.4.8 +legacy-api-wrap==1.4.1 +llvmlite==0.44.0 +MarkupSafe==3.0.2 +matplotlib==3.10.3 +natsort==8.4.0 +networkx==3.4.2 +numba==0.61.2 +numpy==2.2.6 +packaging==25.0 +pandas==2.3.0 +patsy==1.0.1 +pillow==11.2.1 +pycparser==2.22 +pynndescent==0.5.13 +pyparsing==3.2.3 +python-dateutil==2.9.0.post0 +pytz==2025.2 +rpy2==3.6.1 +rpy2-rinterface==3.6.1 +rpy2-robjects==3.6.1 +scanpy==1.11.2 +scikit-learn==1.7.0 +scikit-misc==0.5.1 +scipy==1.15.3 +seaborn==0.13.2 +session-info2==0.1.2 +six==1.17.0 +statsmodels==0.14.4 +threadpoolctl==3.6.0 +tqdm==4.67.1 +typing_extensions==4.14.0 +tzdata==2025.2 +tzlocal==5.3.1 +umap-learn==0.5.7 diff --git a/omicsdm-server/pipelines/snakemake/all/rules/renv.smk b/omicsdm-server/pipelines/snakemake/all/rules/renv.smk new file mode 100644 index 0000000..cb047dc --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/rules/renv.smk @@ -0,0 +1,38 @@ +# Rules: renv +# +# All Rules related to the R package `renv` +# +# Snakefile heavily inspired by: +# https://github.com/lachlandeer/snakemake-econ-r + +# --- renv rules --- # + +## renv_install: installs renv onto machine +rule renv_install: + shell: + "{runR} src/lib/install_renv.R" + +## renv_consent: permission for renv to write files to system +rule renv_consent: + shell: + "R -e 'renv::consent(provided = TRUE)'" + +## renv_install: initialize a renv environment for this project +rule renv_init: + shell: + "R -e 'renv::init(bioconductor = TRUE)'" + +## renv_snap : Look for new R packages in files & archives them +rule renv_snap: + shell: + "R -e 'renv::snapshot()'" + +## renv_restore: Installs archived packages onto a new machine +rule renv_restore: + shell: + "R -e 'renv::restore()'" + +## renv_update: Update R packages to most recent +rule renv_update: + shell: + "R -e 'renv::update()'" diff --git a/omicsdm-server/pipelines/snakemake/all/src/deseq2/deseq2.R b/omicsdm-server/pipelines/snakemake/all/src/deseq2/deseq2.R new file mode 120000 index 0000000..c0ff045 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/deseq2/deseq2.R @@ -0,0 +1 @@ +../../../deseq2/src/deseq2.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess.R b/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess.R new file mode 120000 index 0000000..ac280e5 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess.R @@ -0,0 +1 @@ +../../../deseq2/src/get_data_and_preprocess.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess_new.R b/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess_new.R new file mode 120000 index 0000000..cbd3b57 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess_new.R @@ -0,0 +1 @@ +../../../deseq2/src/get_data_and_preprocess_new.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea/fgsea.R b/omicsdm-server/pipelines/snakemake/all/src/fgsea/fgsea.R new file mode 120000 index 0000000..c293d29 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/fgsea/fgsea.R @@ -0,0 +1 @@ +../../../fgsea/src/fgsea.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea/get_data.R b/omicsdm-server/pipelines/snakemake/all/src/fgsea/get_data.R new file mode 120000 index 0000000..e3210fb --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/fgsea/get_data.R @@ -0,0 +1 @@ +../../../fgsea/src/get_data.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea/reactome2gmt.R b/omicsdm-server/pipelines/snakemake/all/src/fgsea/reactome2gmt.R new file mode 120000 index 0000000..758ca94 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/fgsea/reactome2gmt.R @@ -0,0 +1 @@ +../../../fgsea/src/reactome2gmt.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea_wrapper.R b/omicsdm-server/pipelines/snakemake/all/src/fgsea_wrapper.R new file mode 100644 index 0000000..2d28b77 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/fgsea_wrapper.R @@ -0,0 +1,66 @@ +#!/usr/bin/env Rscript + +# This is a wrapper script for the all pipeline +# It runs the original fgsea.R and then generates significant_genesets.gmt + +# Source the original fgsea.R script +print("Running fgsea analysis...") +source("src/fgsea/fgsea.R") + +# After fgsea completes, extract significant gene sets and create a GMT file +print("Creating significant gene sets GMT file...") + +library(data.table) +library(dplyr) + +# Find all fgsea results files +result_files <- Sys.glob("out/results/*_fgsea.tsv") + +if (length(result_files) == 0) { + stop("No FGSEA result files found") +} + +# Combine all significant results +all_significant <- data.frame() +for (file in result_files) { + res <- fread(file) + # Filter for significant results (padj < 0.05) + sig <- res[padj < 0.05] + if (nrow(sig) > 0) { + all_significant <- rbind(all_significant, sig) + } +} + +# Remove duplicates +all_significant <- unique(all_significant, by = "pathway") + +# Create GMT file +gmt_file <- "out/results/fgsea/significant_genesets.gmt" +dir.create(dirname(gmt_file), recursive = TRUE, showWarnings = FALSE) + +# Write GMT format: pathway_name \t description \t gene1 \t gene2 \t ... +write_gmt <- function(df, output_file) { + con <- file(output_file, "w") + for (i in 1:nrow(df)) { + pathway_name <- df$pathway[i] + # Use pathway name as description too + description <- pathway_name + # Get genes from the leadingEdge column (it's a list) + genes <- unlist(df$leadingEdge[i]) + # Write in GMT format + line <- paste(c(pathway_name, description, genes), collapse = "\t") + writeLines(line, con) + } + close(con) +} + +if (nrow(all_significant) > 0) { + write_gmt(all_significant, gmt_file) + print(paste("Created significant gene sets file with", nrow(all_significant), "pathways")) +} else { + # Create empty file if no significant results + file.create(gmt_file) + print("No significant gene sets found, created empty GMT file") +} + +print("FGSEA wrapper completed successfully") diff --git a/omicsdm-server/pipelines/snakemake/all/src/gsva/get_data.sh b/omicsdm-server/pipelines/snakemake/all/src/gsva/get_data.sh new file mode 120000 index 0000000..24c6424 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/gsva/get_data.sh @@ -0,0 +1 @@ +../../../gsva/src/get_data.sh \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/gsva/sc_genesets_scoring_gsva.py b/omicsdm-server/pipelines/snakemake/all/src/gsva/sc_genesets_scoring_gsva.py new file mode 120000 index 0000000..e276fdd --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/gsva/sc_genesets_scoring_gsva.py @@ -0,0 +1 @@ +../../../gsva/src/sc_genesets_scoring_gsva.py \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/lib/build_report.R b/omicsdm-server/pipelines/snakemake/all/src/lib/build_report.R new file mode 120000 index 0000000..33e75ed --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/lib/build_report.R @@ -0,0 +1 @@ +../../../deseq2/src/lib/build_report.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/lib/install_renv.R b/omicsdm-server/pipelines/snakemake/all/src/lib/install_renv.R new file mode 120000 index 0000000..40d2a17 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/lib/install_renv.R @@ -0,0 +1 @@ +../../../deseq2/src/lib/install_renv.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/report/index.Rmd b/omicsdm-server/pipelines/snakemake/all/src/report/index.Rmd new file mode 120000 index 0000000..57d460a --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/report/index.Rmd @@ -0,0 +1 @@ +../../../deseq2/src/report/index.Rmd \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/report/libs.R b/omicsdm-server/pipelines/snakemake/all/src/report/libs.R new file mode 120000 index 0000000..1ad3f44 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/report/libs.R @@ -0,0 +1 @@ +../../../deseq2/src/report/libs.R \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/get_data.sh b/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/get_data.sh new file mode 120000 index 0000000..556653c --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/get_data.sh @@ -0,0 +1 @@ +../../../sc_normalisation/src/get_data.sh \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/scRNA_normalisation.py b/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/scRNA_normalisation.py new file mode 120000 index 0000000..74233df --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/scRNA_normalisation.py @@ -0,0 +1 @@ +../../../sc_normalisation/src/scRNA_normalisation.py \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/z_scoring/get_data.sh b/omicsdm-server/pipelines/snakemake/all/src/z_scoring/get_data.sh new file mode 120000 index 0000000..4e77af7 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/z_scoring/get_data.sh @@ -0,0 +1 @@ +../../../z_scoring/src/get_data.sh \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/z_scoring/sc_genesets_z_scoring.py b/omicsdm-server/pipelines/snakemake/all/src/z_scoring/sc_genesets_z_scoring.py new file mode 120000 index 0000000..567b500 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/all/src/z_scoring/sc_genesets_z_scoring.py @@ -0,0 +1 @@ +../../../z_scoring/src/sc_genesets_z_scoring.py \ No newline at end of file From 77ed4956b2f98a26292fa9d7c50b3ce119dfc42a Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 29 Dec 2025 13:35:44 +0000 Subject: [PATCH 3/6] Fix symlinks and Snakefile for combined pipeline Co-authored-by: IvoLeist <28399610+IvoLeist@users.noreply.github.com> --- omicsdm-server/pipelines/snakemake/all/Snakefile | 2 +- omicsdm-server/pipelines/snakemake/all/config/deseq2.json | 2 +- omicsdm-server/pipelines/snakemake/all/config/fgsea.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/omicsdm-server/pipelines/snakemake/all/Snakefile b/omicsdm-server/pipelines/snakemake/all/Snakefile index 87a5b13..90b965e 100644 --- a/omicsdm-server/pipelines/snakemake/all/Snakefile +++ b/omicsdm-server/pipelines/snakemake/all/Snakefile @@ -15,7 +15,7 @@ rule report: input: # Outputs from all pipelines deseq2_results="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", - fgsea_results=directory("out/results/fgsea"), + fgsea_results="out/results/fgsea/significant_genesets.gmt", sc_norm_results="out/results/sc_normalisation/normalised.h5ad", z_scoring_results="out/results/z_scoring/z-scored.h5ad", gsva_results="out/results/gsva/gsva-scored.h5ad", diff --git a/omicsdm-server/pipelines/snakemake/all/config/deseq2.json b/omicsdm-server/pipelines/snakemake/all/config/deseq2.json index 8c6b234..7b1f5f5 120000 --- a/omicsdm-server/pipelines/snakemake/all/config/deseq2.json +++ b/omicsdm-server/pipelines/snakemake/all/config/deseq2.json @@ -1 +1 @@ -../../../deseq2/config/deseq2.json \ No newline at end of file +../../deseq2/config/deseq2.json \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/config/fgsea.json b/omicsdm-server/pipelines/snakemake/all/config/fgsea.json index 9599773..a9cec72 120000 --- a/omicsdm-server/pipelines/snakemake/all/config/fgsea.json +++ b/omicsdm-server/pipelines/snakemake/all/config/fgsea.json @@ -1 +1 @@ -../../../fgsea/config/fgsea.json \ No newline at end of file +../../fgsea/config/fgsea.json \ No newline at end of file From d208f1abd10391e06dc00d41f99d1e63ec720bfc Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Mon, 29 Dec 2025 13:37:06 +0000 Subject: [PATCH 4/6] Add comprehensive README for combined pipeline Co-authored-by: IvoLeist <28399610+IvoLeist@users.noreply.github.com> --- .../pipelines/snakemake/all/README.md | 187 +++++++++++++++++- 1 file changed, 177 insertions(+), 10 deletions(-) diff --git a/omicsdm-server/pipelines/snakemake/all/README.md b/omicsdm-server/pipelines/snakemake/all/README.md index 0966390..644d19b 100644 --- a/omicsdm-server/pipelines/snakemake/all/README.md +++ b/omicsdm-server/pipelines/snakemake/all/README.md @@ -1,16 +1,183 @@ -Goal: -One docker container image that is able to run the entire pipeline +# Combined Pipeline for Bulk and Single-cell RNA-seq Analysis -Bulk RNA-seq: +## Goal -1. DESeq2 -2. FGSEA (DESeq2 output as input) +One Docker container image that is able to run the entire pipeline, integrating both bulk RNA-seq and single-cell RNA-seq analyses. -Single-cell RNA-seq: +## Pipeline Overview -3. sc_normalisation +### Bulk RNA-seq Pipeline +1. **DESeq2** - Differential expression analysis +2. **FGSEA** - Functional gene set enrichment analysis (uses DESeq2 output) -Use signifcant gene sets from FGSEA as input for: +### Single-cell RNA-seq Pipeline +3. **sc_normalisation** - Single-cell data normalization -4.a z_scoring -4.b gsva +### Gene Set Scoring Pipelines +Uses significant gene sets from FGSEA as input for: +4. **z_scoring** - Z-score based gene set scoring +5. **gsva** - GSVA gene set scoring + +## Pipeline Dependencies + +``` +DESeq2 → FGSEA → z_scoring + ↘ +sc_normalisation → gsva +``` + +- FGSEA depends on DESeq2 output +- z_scoring and gsva both depend on: + - FGSEA significant gene sets output + - sc_normalisation normalized data + +## Directory Structure + +``` +all/ +├── Dockerfile # Combined Docker image with R and Python +├── docker-compose.yaml # Docker Compose configuration +├── Snakefile # Main Snakemake workflow +├── makefile # Build and run commands +├── requirements.txt # Python dependencies +├── renv.lock # R dependencies +├── config/ # Configuration files for each pipeline +│ ├── deseq2.json +│ ├── fgsea.json +│ ├── sc_normalisation.json +│ ├── z_scoring.json +│ └── gsva.json +├── src/ # Source scripts (symlinked from individual pipelines) +│ ├── deseq2/ +│ ├── fgsea/ +│ ├── sc_normalisation/ +│ ├── z_scoring/ +│ ├── gsva/ +│ ├── lib/ +│ └── report/ +└── rules/ # Snakemake rules + └── renv.smk +``` + +## Building the Docker Image + +```bash +make build +``` + +Or manually: + +```bash +docker build -t omicsdm-all-pipeline:latest . +``` + +## Running the Pipeline + +### Using Make + +```bash +# Run the complete pipeline +make run + +# Open a shell in the container +make shell + +# Clean output directories +make clean +``` + +### Using Docker Directly + +```bash +docker run --rm \ + -v $(PWD)/Snakefile:/home/Snakefile:ro \ + -v $(PWD)/src:/home/src:ro \ + -v $(PWD)/config:/home/config:ro \ + -v $(PWD)/docker-out:/home/out \ + --add-host minio.omicsdm.cnag.dev:172.16.10.112 \ + -it omicsdm-all-pipeline:latest /home/venv/bin/snakemake -F +``` + +## Configuration + +Each pipeline component requires its own configuration file in the `config/` directory: + +- `deseq2.json` - DESeq2 analysis configuration +- `fgsea.json` - FGSEA analysis configuration +- `sc_normalisation.json` - Single-cell normalization configuration +- `z_scoring.json` - Z-scoring configuration +- `gsva.json` - GSVA configuration + +## Outputs + +The pipeline generates outputs in the following structure: + +``` +out/ +├── results/ +│ ├── deseq2/ # DESeq2 analysis results +│ ├── fgsea/ # FGSEA results including significant_genesets.gmt +│ ├── sc_normalisation/ # Normalized single-cell data +│ ├── z_scoring/ # Z-score results +│ └── gsva/ # GSVA results +├── _main.html # Combined report +└── _book/ # Report book directory +``` + +## Key Features + +1. **Single Docker Image**: All dependencies (R, Python, Bioconductor packages, Python packages) in one container +2. **Snakemake Orchestration**: Automatic dependency management and parallel execution +3. **Modular Design**: Each pipeline component is independent but integrated +4. **Reproducible**: Version-controlled dependencies via renv.lock and requirements.txt + +## Technical Details + +### Docker Image +- Base: rocker/r-ver:4.4.0 +- R version: 4.4.0 +- Python: 3.10 +- Includes: Snakemake, awscli, R packages (DESeq2, fgsea, etc.), Python packages (scanpy, anndata, etc.) + +### Dependencies +- **R packages**: Managed via renv (see renv.lock) +- **Python packages**: Listed in requirements.txt +- **System packages**: Defined in Dockerfile + +## Troubleshooting + +### Dry Run +Test the pipeline structure without execution: + +```bash +cd /path/to/all +snakemake --dry-run -j1 +``` + +### View DAG +Visualize the pipeline workflow: + +```bash +snakemake --dag | dot -Tpdf > dag.pdf +``` + +## Development + +### Adding New Pipeline Steps + +1. Create source scripts in appropriate subdirectory under `src/` +2. Add rule to `Snakefile` +3. Update configuration if needed +4. Test with `snakemake --dry-run` + +### Updating Dependencies + +**R packages:** +```bash +R -e 'renv::snapshot()' +``` + +**Python packages:** +```bash +pip freeze > requirements.txt +``` From ef723aa88dd338a743be8fd079077358ad49f5e8 Mon Sep 17 00:00:00 2001 From: Ivo Leist Date: Fri, 2 Jan 2026 15:12:06 +0100 Subject: [PATCH 5/6] bulk_sc_pipeline deseq2 working --- .../pipelines/snakemake/all/.Rprofile | 1 - .../pipelines/snakemake/all/Snakefile | 220 - .../pipelines/snakemake/bulk_sc/.Rprofile | 14 + .../snakemake/{all => bulk_sc}/.dockerignore | 0 .../snakemake/{all => bulk_sc}/.gitignore | 0 .../snakemake/{all => bulk_sc}/.renvignore | 0 .../snakemake/{all => bulk_sc}/Dockerfile | 9 +- .../snakemake/{all => bulk_sc}/README.md | 6 +- .../pipelines/snakemake/bulk_sc/Snakefile | 218 + .../{all => bulk_sc}/config/deseq2.json | 0 .../{all => bulk_sc}/config/fgsea.json | 0 .../{all => bulk_sc}/config/gsva.json | 0 .../config/sc_normalisation.json | 0 .../{all => bulk_sc}/config/z_scoring.json | 0 .../{all => bulk_sc}/docker-compose.yaml | 0 .../snakemake/{all => bulk_sc}/makefile | 0 .../pipelines/snakemake/bulk_sc/renv.lock | 7938 +++++++++++++++++ .../{all/renv.lock => bulk_sc/renv.lock_bk} | 0 .../{all => bulk_sc}/requirements.txt | 0 .../snakemake/{all => bulk_sc}/rules/renv.smk | 0 .../src/deseq2/data_preprocess.R} | 0 .../{all => bulk_sc}/src/deseq2/deseq2.R | 0 .../src/deseq2/get_data_and_preprocess.R | 0 .../src/deseq2/split_into_input_files.sh | 53 + .../{all => bulk_sc}/src/fgsea/fgsea.R | 0 .../{all => bulk_sc}/src/fgsea/get_data.R | 0 .../{all => bulk_sc}/src/fgsea/reactome2gmt.R | 0 .../{all => bulk_sc}/src/fgsea_wrapper.R | 0 .../{all => bulk_sc}/src/gsva/get_data.sh | 0 .../src/gsva/sc_genesets_scoring_gsva.py | 0 .../{all => bulk_sc}/src/lib/build_report.R | 0 .../{all => bulk_sc}/src/lib/install_renv.R | 0 .../{all => bulk_sc}/src/report/index.Rmd | 0 .../{all => bulk_sc}/src/report/libs.R | 0 .../src/sc_normalisation/get_data.sh | 0 .../sc_normalisation/scRNA_normalisation.py | 0 .../src/z_scoring/get_data.sh | 0 .../src/z_scoring/sc_genesets_z_scoring.py | 0 .../snakemake/deseq2/config/deseq2.json | 26 +- .../pipelines/snakemake/deseq2/src/deseq2.R | 121 +- .../deseq2/src/get_data_and_preprocess_new.R | 110 +- .../pipelines/snakemake/fgsea/src/fgsea.R | 35 +- 42 files changed, 8380 insertions(+), 371 deletions(-) delete mode 100644 omicsdm-server/pipelines/snakemake/all/.Rprofile delete mode 100644 omicsdm-server/pipelines/snakemake/all/Snakefile create mode 100644 omicsdm-server/pipelines/snakemake/bulk_sc/.Rprofile rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/.dockerignore (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/.gitignore (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/.renvignore (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/Dockerfile (84%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/README.md (98%) create mode 100644 omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/config/deseq2.json (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/config/fgsea.json (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/config/gsva.json (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/config/sc_normalisation.json (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/config/z_scoring.json (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/docker-compose.yaml (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/makefile (100%) create mode 100644 omicsdm-server/pipelines/snakemake/bulk_sc/renv.lock rename omicsdm-server/pipelines/snakemake/{all/renv.lock => bulk_sc/renv.lock_bk} (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/requirements.txt (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/rules/renv.smk (100%) rename omicsdm-server/pipelines/snakemake/{all/src/deseq2/get_data_and_preprocess_new.R => bulk_sc/src/deseq2/data_preprocess.R} (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/deseq2/deseq2.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/deseq2/get_data_and_preprocess.R (100%) create mode 100644 omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/split_into_input_files.sh rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/fgsea/fgsea.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/fgsea/get_data.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/fgsea/reactome2gmt.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/fgsea_wrapper.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/gsva/get_data.sh (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/gsva/sc_genesets_scoring_gsva.py (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/lib/build_report.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/lib/install_renv.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/report/index.Rmd (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/report/libs.R (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/sc_normalisation/get_data.sh (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/sc_normalisation/scRNA_normalisation.py (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/z_scoring/get_data.sh (100%) rename omicsdm-server/pipelines/snakemake/{all => bulk_sc}/src/z_scoring/sc_genesets_z_scoring.py (100%) diff --git a/omicsdm-server/pipelines/snakemake/all/.Rprofile b/omicsdm-server/pipelines/snakemake/all/.Rprofile deleted file mode 100644 index 81b960f..0000000 --- a/omicsdm-server/pipelines/snakemake/all/.Rprofile +++ /dev/null @@ -1 +0,0 @@ -source("renv/activate.R") diff --git a/omicsdm-server/pipelines/snakemake/all/Snakefile b/omicsdm-server/pipelines/snakemake/all/Snakefile deleted file mode 100644 index 90b965e..0000000 --- a/omicsdm-server/pipelines/snakemake/all/Snakefile +++ /dev/null @@ -1,220 +0,0 @@ -PROJ_NAME = "all" - -# --- Variable Declarations ---- # -runR = "Rscript --no-save --no-restore --verbose" -runPython = "venv/bin/python3" -logAll = "2>&1" - - -rule all: - input: - report_html=f"out/_main.html", - - -rule report: - input: - # Outputs from all pipelines - deseq2_results="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", - fgsea_results="out/results/fgsea/significant_genesets.gmt", - sc_norm_results="out/results/sc_normalisation/normalised.h5ad", - z_scoring_results="out/results/z_scoring/z-scored.h5ad", - gsva_results="out/results/gsva/gsva-scored.h5ad", - rmd="src/report/index.Rmd", - output: - html="out/_main.html", - book=directory("out/_book"), - log: - "log/report.log", - shell: - """ - cp {input.rmd} out/. - {runR} src/lib/build_report.R | tee {log} - """ - - -# --- Bulk RNA-seq Pipeline --- # - -# 1. DESeq2 Analysis -rule deseq2_analysis: - input: - rds_obj1="out/rds/deseq2_obj1.rds", - rds_obj2="out/rds/deseq2_obj2.rds", - config="config/deseq2.json", - output: - out3="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", - out5="out/results/deseq2/sessionInfo/sessionInfo.txt", - log: - "log/deseq2_analysis.log", - shell: - """ - mkdir -p out/results/deseq2/sessionInfo - {runR} src/deseq2/deseq2.R | tee {log} - """ - - -rule deseq2_get_data: - input: - config="config/deseq2.json", - output: - rds_obj1="out/rds/deseq2_obj1.rds", - rds_obj2="out/rds/deseq2_obj2.rds", - log: - "log/deseq2_get_data.log", - shell: - """ - mkdir -p out/rds - {runR} src/deseq2/get_data_and_preprocess.R {input.config} | tee {log} - """ - - -# 2. FGSEA Analysis (depends on DESeq2 output) -rule fgsea_analysis: - input: - in1="in/fgsea/results.tar.gz", - in2="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", - config="config/fgsea.json", - # Ensure DESeq2 completes first - deseq2_done="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", - output: - out7="out/results/fgsea/sessionInfo/sessionInfo.txt", - out8="out/results/fgsea/sessionInfo/platform.rds", - out9="out/results/fgsea/sessionInfo/packages.rds", - significant_genesets="out/results/fgsea/significant_genesets.gmt", - log: - "log/fgsea_analysis.log", - shell: - """ - mkdir -p out/results/fgsea/sessionInfo - {runR} src/fgsea_wrapper.R | tee {log} - """ - - -rule fgsea_get_data: - input: - config="config/fgsea.json", - output: - out1="in/fgsea/results.tar.gz", - out4="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", - log: - "log/fgsea_get_data.log", - shell: - """ - mkdir -p in/fgsea out/tmp - {runR} src/fgsea/get_data.R {input.config} | tee {log} - """ - - -# --- Single-cell RNA-seq Pipeline --- # - -# 3. Single-cell Normalisation -rule sc_normalisation: - input: - in1="in/sc_normalisation/data.h5ad", - config="config/sc_normalisation.json", - output: - out1="out/results/sc_normalisation/normalised.h5ad", - log: - "log/sc_normalisation.log", - shell: - """ - mkdir -p out/results/sc_normalisation - {runPython} src/sc_normalisation/scRNA_normalisation.py \ - --path {input.in1} | tee {log} - cp normalised.h5ad {output.out1} - """ - - -rule sc_normalisation_get_data: - input: - config="config/sc_normalisation.json", - output: - out1="in/sc_normalisation/data.h5ad", - log: - "log/sc_normalisation_get_data.log", - shell: - """ - mkdir -p in/sc_normalisation - bash src/sc_normalisation/get_data.sh | tee {log} - """ - - -# --- Gene Set Scoring Pipelines (depend on FGSEA significant gene sets) --- # - -# 4.a Z-scoring -rule z_scoring: - input: - original_h5ad="in/z_scoring/original.h5ad", - normalised_h5ad="out/results/sc_normalisation/normalised.h5ad", - gene_sets="out/results/fgsea/significant_genesets.gmt", - config="config/z_scoring.json", - output: - out1="out/results/z_scoring/z_scores.tsv", - out2="out/results/z_scoring/z-scored.h5ad", - log: - "log/z_scoring.log", - shell: - """ - mkdir -p out/results/z_scoring - {runPython} src/z_scoring/sc_genesets_z_scoring.py \ - --original_h5ad {input.original_h5ad} \ - --normalised_h5ad {input.normalised_h5ad} \ - --gene_sets {input.gene_sets} | tee {log} - cp z_scores.tsv {output.out1} - cp z-scored.h5ad {output.out2} - """ - - -rule z_scoring_get_data: - input: - config="config/z_scoring.json", - output: - out1="in/z_scoring/original.h5ad", - log: - "log/z_scoring_get_data.log", - shell: - """ - mkdir -p in/z_scoring - bash src/z_scoring/get_data.sh | tee {log} - """ - - -# 4.b GSVA -rule gsva: - input: - original_h5ad="in/gsva/original.h5ad", - normalised_h5ad="out/results/sc_normalisation/normalised.h5ad", - gene_sets="out/results/fgsea/significant_genesets.gmt", - config="config/gsva.json", - output: - out1="out/results/gsva/gsva_scores.tsv", - out2="out/results/gsva/gsva-scored.h5ad", - log: - "log/gsva.log", - shell: - """ - mkdir -p out/results/gsva - {runPython} src/gsva/sc_genesets_scoring_gsva.py \ - --original_h5ad {input.original_h5ad} \ - --normalised_h5ad {input.normalised_h5ad} \ - --gene_sets {input.gene_sets} | tee {log} - cp gsva_scores.tsv {output.out1} - cp gsva-scored.h5ad {output.out2} - """ - - -rule gsva_get_data: - input: - config="config/gsva.json", - output: - out1="in/gsva/original.h5ad", - log: - "log/gsva_get_data.log", - shell: - """ - mkdir -p in/gsva - bash src/gsva/get_data.sh | tee {log} - """ - - -# 2. Other rules -include: "rules/renv.smk" diff --git a/omicsdm-server/pipelines/snakemake/bulk_sc/.Rprofile b/omicsdm-server/pipelines/snakemake/bulk_sc/.Rprofile new file mode 100644 index 0000000..1b7eeab --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/.Rprofile @@ -0,0 +1,14 @@ +source("renv/activate.R") +options(renv.config.pak.enabled = TRUE) + +# Configure BiocManager to use Posit Package Manager +options(BioC_mirror = "https://packagemanager.posit.co/bioconductor/2025-12-30") + +# Configure BiocManager to load its configuration from Package Manager +options(BIOCONDUCTOR_CONFIG_FILE = "https://packagemanager.posit.co/bioconductor/2025-12-30/config.yaml") + +# Set the Bioconductor version to prevent defaulting to a newer version +Sys.setenv("R_BIOC_VERSION" = "3.22") + +# Configure a CRAN snapshot compatible with Bioconductor 3.22 +options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2025-12-30")) \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/.dockerignore b/omicsdm-server/pipelines/snakemake/bulk_sc/.dockerignore similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/.dockerignore rename to omicsdm-server/pipelines/snakemake/bulk_sc/.dockerignore diff --git a/omicsdm-server/pipelines/snakemake/all/.gitignore b/omicsdm-server/pipelines/snakemake/bulk_sc/.gitignore similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/.gitignore rename to omicsdm-server/pipelines/snakemake/bulk_sc/.gitignore diff --git a/omicsdm-server/pipelines/snakemake/all/.renvignore b/omicsdm-server/pipelines/snakemake/bulk_sc/.renvignore similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/.renvignore rename to omicsdm-server/pipelines/snakemake/bulk_sc/.renvignore diff --git a/omicsdm-server/pipelines/snakemake/all/Dockerfile b/omicsdm-server/pipelines/snakemake/bulk_sc/Dockerfile similarity index 84% rename from omicsdm-server/pipelines/snakemake/all/Dockerfile rename to omicsdm-server/pipelines/snakemake/bulk_sc/Dockerfile index 3794f46..72c0cd6 100644 --- a/omicsdm-server/pipelines/snakemake/all/Dockerfile +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/Dockerfile @@ -1,17 +1,18 @@ -FROM rocker/r-ver:4.4.0 +FROM rocker/r-ver:4.5.2 # Install system dependencies for both R and Python packages RUN apt-get update && apt-get install -y \ curl \ jq \ python3 \ - python3.10-venv \ + python3.12-venv \ python3-pip \ libxml2 \ pandoc \ git \ libfontconfig1-dev \ libfreetype6-dev \ + libgit2-dev \ libicu-dev \ libglpk-dev \ libpng-dev \ @@ -33,8 +34,8 @@ RUN apt-get update && apt-get install -y \ # Set BLAS and LAPACK to libblas RUN ARCH=$(uname -m) && \ - update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/blas/libblas.so.3" && \ - update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/lapack/liblapack.so.3" + update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/blas/libblas.so.3" && \ + update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/lapack/liblapack.so.3" # Install Snakemake and Python packages RUN python3 -m venv /home/venv diff --git a/omicsdm-server/pipelines/snakemake/all/README.md b/omicsdm-server/pipelines/snakemake/bulk_sc/README.md similarity index 98% rename from omicsdm-server/pipelines/snakemake/all/README.md rename to omicsdm-server/pipelines/snakemake/bulk_sc/README.md index 644d19b..33b1100 100644 --- a/omicsdm-server/pipelines/snakemake/all/README.md +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/README.md @@ -20,11 +20,7 @@ Uses significant gene sets from FGSEA as input for: ## Pipeline Dependencies -``` -DESeq2 → FGSEA → z_scoring - ↘ -sc_normalisation → gsva -``` + - FGSEA depends on DESeq2 output - z_scoring and gsva both depend on: diff --git a/omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile b/omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile new file mode 100644 index 0000000..d8fa915 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile @@ -0,0 +1,218 @@ +PROJ_NAME = "all" + +# --- Variable Declarations ---- # +runR = "Rscript --no-save --no-restore --verbose" +runPython = "venv/bin/python3" +logAll = "2>&1" + + +rule all: + input: + report_html=f"out/_main.html", + + +rule report: + input: + # Outputs from all pipelines + deseq2_results="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", + # fgsea_results="out/results/fgsea/significant_genesets.gmt", + # sc_norm_results="out/results/sc_normalisation/normalised.h5ad", + # z_scoring_results="out/results/z_scoring/z-scored.h5ad", + # gsva_results="out/results/gsva/gsva-scored.h5ad", + rmd="src/report/index.Rmd", + output: + html="out/_main.html", + book=directory("out/_book"), + log: + "log/report.log", + shell: + """ + cp {input.rmd} out/. + {runR} src/lib/build_report.R | tee {log} + """ + + +# --- Bulk RNA-seq Pipeline --- # + +# 1. DESeq2 Analysis +rule deseq2_preprocess_data: + input: + config="config/deseq2.json", + output: + rds_obj1="out/rds/deseq2_obj1.rds", + rds_obj2="out/rds/deseq2_obj2.rds", + log: + "log/deseq2_get_data.log", + shell: + """ + mkdir -p out/rds + {runR} src/deseq2/data_preprocess.R {input.config} | tee {log} + """ + +rule deseq2_analysis: + input: + rds_obj1="out/rds/deseq2_obj1.rds", + rds_obj2="out/rds/deseq2_obj2.rds", + config="config/deseq2.json", + output: + out3="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", + out5="out/results/deseq2/sessionInfo/sessionInfo.txt", + log: + "log/deseq2_analysis.log", + shell: + """ + mkdir -p out/results/deseq2/sessionInfo + {runR} src/deseq2/deseq2.R | tee {log} + """ + +# 2. FGSEA Analysis (depends on DESeq2 output) +# rule fgsea_analysis: +# input: +# in1="in/fgsea/results.tar.gz", +# in2="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", +# config="config/fgsea.json", +# # Ensure DESeq2 completes first +# deseq2_done="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", +# output: +# out7="out/results/fgsea/sessionInfo/sessionInfo.txt", +# out8="out/results/fgsea/sessionInfo/platform.rds", +# out9="out/results/fgsea/sessionInfo/packages.rds", +# significant_genesets="out/results/fgsea/significant_genesets.gmt", +# log: +# "log/fgsea_analysis.log", +# shell: +# """ +# mkdir -p out/results/fgsea/sessionInfo +# {runR} src/fgsea_wrapper.R | tee {log} +# """ + + +# rule fgsea_get_data: +# input: +# config="config/fgsea.json", +# output: +# out1="in/fgsea/results.tar.gz", +# out4="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", +# log: +# "log/fgsea_get_data.log", +# shell: +# """ +# mkdir -p in/fgsea out/tmp +# {runR} src/fgsea/get_data.R {input.config} | tee {log} +# """ + + +# # --- Single-cell RNA-seq Pipeline --- # + +# # 3. Single-cell Normalisation +# rule sc_normalisation: +# input: +# in1="in/sc_normalisation/data.h5ad", +# config="config/sc_normalisation.json", +# output: +# out1="out/results/sc_normalisation/normalised.h5ad", +# log: +# "log/sc_normalisation.log", +# shell: +# """ +# mkdir -p out/results/sc_normalisation +# {runPython} src/sc_normalisation/scRNA_normalisation.py \ +# --path {input.in1} | tee {log} +# cp normalised.h5ad {output.out1} +# """ + + +# rule sc_normalisation_get_data: +# input: +# config="config/sc_normalisation.json", +# output: +# out1="in/sc_normalisation/data.h5ad", +# log: +# "log/sc_normalisation_get_data.log", +# shell: +# """ +# mkdir -p in/sc_normalisation +# bash src/sc_normalisation/get_data.sh | tee {log} +# """ + + +# # --- Gene Set Scoring Pipelines (depend on FGSEA significant gene sets) --- # + +# # 4.a Z-scoring +# rule z_scoring: +# input: +# original_h5ad="in/z_scoring/original.h5ad", +# normalised_h5ad="out/results/sc_normalisation/normalised.h5ad", +# gene_sets="out/results/fgsea/significant_genesets.gmt", +# config="config/z_scoring.json", +# output: +# out1="out/results/z_scoring/z_scores.tsv", +# out2="out/results/z_scoring/z-scored.h5ad", +# log: +# "log/z_scoring.log", +# shell: +# """ +# mkdir -p out/results/z_scoring +# {runPython} src/z_scoring/sc_genesets_z_scoring.py \ +# --original_h5ad {input.original_h5ad} \ +# --normalised_h5ad {input.normalised_h5ad} \ +# --gene_sets {input.gene_sets} | tee {log} +# cp z_scores.tsv {output.out1} +# cp z-scored.h5ad {output.out2} +# """ + + +# rule z_scoring_get_data: +# input: +# config="config/z_scoring.json", +# output: +# out1="in/z_scoring/original.h5ad", +# log: +# "log/z_scoring_get_data.log", +# shell: +# """ +# mkdir -p in/z_scoring +# bash src/z_scoring/get_data.sh | tee {log} +# """ + + +# # 4.b GSVA +# rule gsva: +# input: +# original_h5ad="in/gsva/original.h5ad", +# normalised_h5ad="out/results/sc_normalisation/normalised.h5ad", +# gene_sets="out/results/fgsea/significant_genesets.gmt", +# config="config/gsva.json", +# output: +# out1="out/results/gsva/gsva_scores.tsv", +# out2="out/results/gsva/gsva-scored.h5ad", +# log: +# "log/gsva.log", +# shell: +# """ +# mkdir -p out/results/gsva +# {runPython} src/gsva/sc_genesets_scoring_gsva.py \ +# --original_h5ad {input.original_h5ad} \ +# --normalised_h5ad {input.normalised_h5ad} \ +# --gene_sets {input.gene_sets} | tee {log} +# cp gsva_scores.tsv {output.out1} +# cp gsva-scored.h5ad {output.out2} +# """ + + +# rule gsva_get_data: +# input: +# config="config/gsva.json", +# output: +# out1="in/gsva/original.h5ad", +# log: +# "log/gsva_get_data.log", +# shell: +# """ +# mkdir -p in/gsva +# bash src/gsva/get_data.sh | tee {log} +# """ + + +# # 2. Other rules +# include: "rules/renv.smk" diff --git a/omicsdm-server/pipelines/snakemake/all/config/deseq2.json b/omicsdm-server/pipelines/snakemake/bulk_sc/config/deseq2.json similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/config/deseq2.json rename to omicsdm-server/pipelines/snakemake/bulk_sc/config/deseq2.json diff --git a/omicsdm-server/pipelines/snakemake/all/config/fgsea.json b/omicsdm-server/pipelines/snakemake/bulk_sc/config/fgsea.json similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/config/fgsea.json rename to omicsdm-server/pipelines/snakemake/bulk_sc/config/fgsea.json diff --git a/omicsdm-server/pipelines/snakemake/all/config/gsva.json b/omicsdm-server/pipelines/snakemake/bulk_sc/config/gsva.json similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/config/gsva.json rename to omicsdm-server/pipelines/snakemake/bulk_sc/config/gsva.json diff --git a/omicsdm-server/pipelines/snakemake/all/config/sc_normalisation.json b/omicsdm-server/pipelines/snakemake/bulk_sc/config/sc_normalisation.json similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/config/sc_normalisation.json rename to omicsdm-server/pipelines/snakemake/bulk_sc/config/sc_normalisation.json diff --git a/omicsdm-server/pipelines/snakemake/all/config/z_scoring.json b/omicsdm-server/pipelines/snakemake/bulk_sc/config/z_scoring.json similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/config/z_scoring.json rename to omicsdm-server/pipelines/snakemake/bulk_sc/config/z_scoring.json diff --git a/omicsdm-server/pipelines/snakemake/all/docker-compose.yaml b/omicsdm-server/pipelines/snakemake/bulk_sc/docker-compose.yaml similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/docker-compose.yaml rename to omicsdm-server/pipelines/snakemake/bulk_sc/docker-compose.yaml diff --git a/omicsdm-server/pipelines/snakemake/all/makefile b/omicsdm-server/pipelines/snakemake/bulk_sc/makefile similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/makefile rename to omicsdm-server/pipelines/snakemake/bulk_sc/makefile diff --git a/omicsdm-server/pipelines/snakemake/bulk_sc/renv.lock b/omicsdm-server/pipelines/snakemake/bulk_sc/renv.lock new file mode 100644 index 0000000..0f558f8 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/renv.lock @@ -0,0 +1,7938 @@ +{ + "R": { + "Version": "4.5.2", + "Repositories": [ + { + "Name": "BioCsoft", + "URL": "https://bioconductor.org/packages/3.22/bioc" + }, + { + "Name": "BioCann", + "URL": "https://bioconductor.org/packages/3.22/data/annotation" + }, + { + "Name": "BioCexp", + "URL": "https://bioconductor.org/packages/3.22/data/experiment" + }, + { + "Name": "BioCworkflows", + "URL": "https://bioconductor.org/packages/3.22/workflows" + }, + { + "Name": "BioCbooks", + "URL": "https://bioconductor.org/packages/3.22/books" + }, + { + "Name": "CRAN", + "URL": "https://packagemanager.posit.co/cran/2025-12-30" + } + ] + }, + "Bioconductor": { + "Version": "3.22" + }, + "Packages": { + "AnnotationDbi": { + "Package": "AnnotationDbi", + "Version": "1.72.0", + "Source": "Bioconductor", + "Title": "Manipulation of SQLite-based annotations in Bioconductor", + "Description": "Implements a user-friendly interface for querying SQLite-based annotation data packages.", + "biocViews": "Annotation, Microarray, Sequencing, GenomeAnnotation", + "URL": "https://bioconductor.org/packages/AnnotationDbi", + "Video": "https://www.youtube.com/watch?v=8qvGNTVz3Ik", + "BugReports": "https://github.com/Bioconductor/AnnotationDbi/issues", + "License": "Artistic-2.0", + "Encoding": "UTF-8", + "Author": "Hervé Pagès, Marc Carlson, Seth Falcon, Nianhua Li", + "Maintainer": "Bioconductor Package Maintainer ", + "Depends": [ + "R (>= 2.7.0)", + "methods", + "stats4", + "BiocGenerics (>= 0.29.2)", + "Biobase (>= 1.17.0)", + "IRanges" + ], + "Imports": [ + "DBI", + "RSQLite", + "S4Vectors (>= 0.9.25)", + "stats", + "KEGGREST" + ], + "Suggests": [ + "utils", + "hgu95av2.db", + "GO.db", + "org.Sc.sgd.db", + "org.At.tair.db", + "RUnit", + "TxDb.Hsapiens.UCSC.hg19.knownGene", + "org.Hs.eg.db", + "reactome.db", + "AnnotationForge", + "graph", + "EnsDb.Hsapiens.v75", + "BiocStyle", + "knitr" + ], + "VignetteBuilder": "knitr", + "Collate": "00RTobjs.R AllGenerics.R AllClasses.R unlist2.R utils.R SQL.R FlatBimap.R AnnDbObj-lowAPI.R Bimap.R GOTerms.R BimapFormatting.R Bimap-envirAPI.R flatten.R methods-AnnotationDb.R methods-SQLiteConnection.R methods-geneCentricDbs.R methods-geneCentricDbs-keys.R methods-ReactomeDb.R methods-OrthologyDb.R loadDb.R createAnnObjs-utils.R createAnnObjs.NCBIORG_DBs.R createAnnObjs.NCBICHIP_DBs.R createAnnObjs.ORGANISM_DB.R createAnnObjs.YEASTCHIP_DB.R createAnnObjs.COELICOLOR_DB.R createAnnObjs.ARABIDOPSISCHIP_DB.R createAnnObjs.MALARIA_DB.R createAnnObjs.YEAST_DB.R createAnnObjs.YEASTNCBI_DB.R createAnnObjs.ARABIDOPSIS_DB.R createAnnObjs.GO_DB.R createAnnObjs.KEGG_DB.R createAnnObjs.PFAM_DB.R AnnDbPkg-templates-common.R AnnDbPkg-checker.R print.probetable.R makeMap.R inpIDMapper.R test_AnnotationDbi_package.R", + "git_url": "https://git.bioconductor.org/packages/AnnotationDbi", + "git_branch": "RELEASE_3_22", + "git_last_commit": "ffdaf5d", + "git_last_commit_date": "2025-10-29", + "Repository": "RSPM", + "NeedsCompilation": "no" + }, + "BH": { + "Package": "BH", + "Version": "1.90.0-1", + "Source": "Repository", + "Type": "Package", + "Title": "Boost C++ Header Files", + "Date": "2025-12-13", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"John W.\", \"Emerson\", role = \"aut\"), person(\"Michael J.\", \"Kane\", role = \"aut\", comment = c(ORCID = \"0000-0003-1899-6662\")))", + "Description": "Boost provides free peer-reviewed portable C++ source libraries. 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authors listed in inst/resources/AUTHORS\"), person(family = \"FriendCode Inc\", role = c(\"cph\", \"ctb\"), comment = \"The gitbook style, with modifications\") )", + "Maintainer": "Yihui Xie ", + "Description": "Output formats and utilities for authoring books and technical documents with R Markdown.", + "License": "GPL-3", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "htmltools (>= 0.3.6)", + "knitr (>= 1.38)", + "rmarkdown (>= 2.14)", + "jquerylib", + "xfun (>= 0.48)", + "tinytex (>= 0.12)", + "yaml (>= 2.1.19)" + ], + "Suggests": [ + "bslib (>= 0.2.4)", + "downlit (>= 0.4.0)", + "htmlwidgets", + "jsonlite", + "curl", + "rstudioapi", + "miniUI", + "rsconnect (>= 1.6.0)", + "servr (>= 0.13)", + "shiny", + "tibble", + "testit (>= 0.9)", + "tufte", + "xml2", + "webshot", + "testthat (>= 3.1.0)", + "withr (>= 2.3.0)" + ], + "URL": "https://github.com/rstudio/bookdown, https://pkgs.rstudio.com/bookdown/", + "BugReports": "https://github.com/rstudio/bookdown/issues", + "SystemRequirements": "Pandoc (>= 1.17.2)", + "RoxygenNote": "7.3.3", + "Encoding": "UTF-8", + "Config/Needs/book": "remotes, webshot, svglite", + "Config/Needs/website": "pkgdown, tidyverse/tidytemplate, rstudio/quillt", + "Config/testthat/edition": "3", + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (ORCID: ), Christophe Dervieux [ctb] (ORCID: ), JJ Allaire [ctb], Albert Kim [ctb], Alessandro Samuel-Rosa [ctb], Andrzej Oles [ctb], Atsushi Yasumoto [ctb] (ORCID: ), Aust Frederik [ctb] (ORCID: ), Bastiaan Quast [ctb], Ben Marwick [ctb], Chester Ismay [ctb], Clifton Franklund [ctb], Daniel Emaasit [ctb], David Shuman [ctb], Dean Attali [ctb], Drew Tyre [ctb], Ellis Valentiner [ctb], Frans van Dunne [ctb], Hadley Wickham [ctb], Jeff Allen [ctb], Jennifer Bryan [ctb], Jonathan McPhers [ctb], JooYoung Seo [ctb] (ORCID: ), Joyce Robbins [ctb], Junwen Huang [ctb], Kevin Cheung [ctb], Kevin Ushey [ctb], Kim Seonghyun [ctb], Kirill Muller [ctb], Luciano Selzer [ctb], Matthew Lincoln [ctb], Maximilian Held [ctb], Michael Sachs [ctb], Michal Bojanowski [ctb], Nathan Werth [ctb], Noam Ross [ctb], Peter Hickey [ctb], Pedro Rafael D. 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similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.", + "License": "GPL (>= 2)", + "URL": "https://github.com/gregfrog/brew", + "BugReports": "https://github.com/gregfrog/brew/issues", + "Suggests": [ + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Repository": "RSPM", + "NeedsCompilation": "no", + "Author": "Jeffrey Horner [aut, cph], Greg Hunt [aut, cre, cph]", + "Maintainer": "Greg Hunt " + }, + "brio": { + "Package": "brio", + "Version": "1.1.5", + "Source": "Repository", + "Title": "Basic R Input Output", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Functions to handle basic input output, these functions always read and write UTF-8 (8-bit Unicode Transformation Format) files and provide more explicit control over line endings.", + "License": "MIT + file LICENSE", + "URL": "https://brio.r-lib.org, https://github.com/r-lib/brio", + "BugReports": "https://github.com/r-lib/brio/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Gábor Csárdi [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "broom": { + "Package": "broom", + "Version": "1.0.11", + "Source": "Repository", + "Type": "Package", + "Title": "Convert Statistical Objects into Tidy Tibbles", + "Authors@R": "c( person(\"David\", \"Robinson\", , \"admiral.david@gmail.com\", role = \"aut\"), person(\"Alex\", \"Hayes\", , \"alexpghayes@gmail.com\", role = \"aut\", comment = c(ORCID = 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'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.", + "License": "MIT + file LICENSE", + "URL": "https://conflicted.r-lib.org/, https://github.com/r-lib/conflicted", + "BugReports": "https://github.com/r-lib/conflicted/issues", + "Depends": [ + "R (>= 3.2)" + ], + "Imports": [ + "cli (>= 3.4.0)", + "memoise", + "rlang (>= 1.0.0)" + ], + "Suggests": [ + "callr", + "covr", + "dplyr", + "Matrix", + "methods", + "pkgload", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, + "cowplot": { + "Package": "cowplot", + "Version": "1.2.0", + "Source": "Repository", + "Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'", + "Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )", + "Description": "Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.", + "URL": "https://wilkelab.org/cowplot/", + "BugReports": "https://github.com/wilkelab/cowplot/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 3.5.2)", + "grid", + "gtable", + "grDevices", + "methods", + "rlang", + "scales" + ], + "License": "GPL-2", + "Suggests": [ + "Cairo", + "covr", + "dplyr", + "forcats", + "gridGraphics (>= 0.4-0)", + "knitr", + "lattice", + "magick", + "maps", + "PASWR", + "patchwork", + "rmarkdown", + "ragg", + "testthat (>= 1.0.0)", + "tidyr", + "vdiffr (>= 0.3.0)", + "VennDiagram" + ], + "VignetteBuilder": "knitr", + "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Claus O. Wilke [aut, cre] (ORCID: )", + "Maintainer": "Claus O. Wilke ", + "Repository": "RSPM" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.2", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "RSPM" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "credentials": { + "Package": "credentials", + "Version": "2.0.3", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Managing SSH and Git Credentials", + "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))", + "Description": "Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.", + "License": "MIT + file LICENSE", + "SystemRequirements": "git (optional)", + "Encoding": "UTF-8", + "Imports": [ + "openssl (>= 1.3)", + "sys (>= 2.1)", + "curl", + "jsonlite", + "askpass" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown" + ], + "RoxygenNote": "7.2.1", + "VignetteBuilder": "knitr", + "Language": "en-US", + "URL": "https://docs.ropensci.org/credentials/ https://r-lib.r-universe.dev/credentials", + "BugReports": "https://github.com/r-lib/credentials/issues", + "NeedsCompilation": "no", + "Author": "Jeroen Ooms [aut, cre] (ORCID: )", + "Maintainer": "Jeroen Ooms ", + "Repository": "RSPM" + }, + "curl": { + "Package": "curl", + "Version": "7.0.0", + "Source": "Repository", + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.73): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "RSPM" + }, + "data.table": { + "Package": "data.table", + "Version": "1.18.0", + "Source": "Repository", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.4.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils (>= 2.13.0)", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\", email=\"j.gorecki@wit.edu.pl\"), person(\"Michael\",\"Chirico\", role=\"aut\", email=\"michaelchirico4@gmail.com\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", email=\"toby.hocking@r-project.org\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Ivan\", \"Krylov\", role=\"aut\", email=\"ikrylov@disroot.org\", comment = c(ORCID=\"0000-0002-0172-3812\")), person(\"Pasha\",\"Stetsenko\", role=\"ctb\"), person(\"Tom\",\"Short\", role=\"ctb\"), person(\"Steve\",\"Lianoglou\", role=\"ctb\"), person(\"Eduard\",\"Antonyan\", role=\"ctb\"), person(\"Markus\",\"Bonsch\", role=\"ctb\"), person(\"Hugh\",\"Parsonage\", role=\"ctb\"), person(\"Scott\",\"Ritchie\", role=\"ctb\"), person(\"Kun\",\"Ren\", role=\"ctb\"), person(\"Xianying\",\"Tan\", role=\"ctb\"), person(\"Rick\",\"Saporta\", role=\"ctb\"), person(\"Otto\",\"Seiskari\", role=\"ctb\"), person(\"Xianghui\",\"Dong\", role=\"ctb\"), person(\"Michel\",\"Lang\", role=\"ctb\"), person(\"Watal\",\"Iwasaki\", role=\"ctb\"), person(\"Seth\",\"Wenchel\", role=\"ctb\"), person(\"Karl\",\"Broman\", role=\"ctb\"), person(\"Tobias\",\"Schmidt\", role=\"ctb\"), person(\"David\",\"Arenburg\", role=\"ctb\"), person(\"Ethan\",\"Smith\", role=\"ctb\"), person(\"Francois\",\"Cocquemas\", role=\"ctb\"), person(\"Matthieu\",\"Gomez\", role=\"ctb\"), person(\"Philippe\",\"Chataignon\", role=\"ctb\"), person(\"Nello\",\"Blaser\", role=\"ctb\"), person(\"Dmitry\",\"Selivanov\", role=\"ctb\"), person(\"Andrey\",\"Riabushenko\", role=\"ctb\"), person(\"Cheng\",\"Lee\", role=\"ctb\"), person(\"Declan\",\"Groves\", role=\"ctb\"), person(\"Daniel\",\"Possenriede\", role=\"ctb\"), person(\"Felipe\",\"Parages\", role=\"ctb\"), person(\"Denes\",\"Toth\", role=\"ctb\"), person(\"Mus\",\"Yaramaz-David\", role=\"ctb\"), person(\"Ayappan\",\"Perumal\", role=\"ctb\"), person(\"James\",\"Sams\", role=\"ctb\"), person(\"Martin\",\"Morgan\", role=\"ctb\"), person(\"Michael\",\"Quinn\", role=\"ctb\"), person(given=\"@javrucebo\", role=\"ctb\", comment=\"GitHub user\"), person(\"Marc\",\"Halperin\", role=\"ctb\"), person(\"Roy\",\"Storey\", role=\"ctb\"), 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role=\"ctb\"), person(\"Reino\", \"Bruner\", role=\"ctb\"), person(given=\"@badasahog\", role=\"ctb\", comment=\"GitHub user\"), person(\"Vinit\", \"Thakur\", role=\"ctb\"), person(\"Mukul\", \"Kumar\", role=\"ctb\"), person(\"Ildikó\", \"Czeller\", role=\"ctb\") )", + "NeedsCompilation": "yes", + "Author": "Tyson Barrett [aut, cre] (ORCID: ), Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut] (ORCID: ), Toby Hocking [aut] (ORCID: ), Benjamin Schwendinger [aut] (ORCID: ), Ivan Krylov [aut] (ORCID: ), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb] (GitHub user), Marc Halperin [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], 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tables as if they are in-memory data frames. 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'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.", + "License": "MIT + file LICENSE", + "URL": "https://httr2.r-lib.org, https://github.com/r-lib/httr2", + "BugReports": "https://github.com/r-lib/httr2/issues", + "Depends": [ + "R (>= 4.1)" + ], + "Imports": [ + "cli (>= 3.0.0)", + "curl (>= 6.4.0)", + "glue", + "lifecycle", + "magrittr", + "openssl", + "R6", + "rappdirs", + "rlang (>= 1.1.0)", + "vctrs (>= 0.6.3)", + "withr" + ], + "Suggests": [ + "askpass", + "bench", + "clipr", + "covr", + "docopt", + "httpuv", + "jose", + "jsonlite", + "knitr", + "later (>= 1.4.0)", + "nanonext", + "otel (>= 0.2.0)", + "otelsdk (>= 0.2.0)", + "paws.common (>= 0.8.0)", + "promises", + "rmarkdown", + "testthat (>= 3.1.8)", + "tibble", + "webfakes (>= 1.4.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "resp-stream, req-perform", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], Maximilian Girlich [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, + "ids": { + "Package": "ids", + "Version": "1.0.1", + "Source": "Repository", + "Title": "Generate Random Identifiers", + "Authors@R": "person(\"Rich\", \"FitzJohn\", role = c(\"aut\", \"cre\"), email = \"rich.fitzjohn@gmail.com\")", + "Description": "Generate random or human readable and pronounceable identifiers.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/richfitz/ids", + "BugReports": "https://github.com/richfitz/ids/issues", + "Imports": [ + "openssl", + "uuid" + ], + "Suggests": [ + "knitr", + "rcorpora", + "rmarkdown", + "testthat" + ], + "RoxygenNote": "6.0.1", + "VignetteBuilder": "knitr", + "NeedsCompilation": "no", + "Author": "Rich FitzJohn [aut, cre]", + "Maintainer": "Rich FitzJohn ", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "ini": { + "Package": "ini", + "Version": "0.3.1", + "Source": "Repository", + "Type": "Package", + "Title": "Read and Write '.ini' Files", + "Date": "2018-05-19", + "Author": "David Valentim Dias", + "Maintainer": "David Valentim Dias ", + "Description": "Parse simple '.ini' configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.", + "License": "GPL-3", + "URL": "https://github.com/dvdscripter/ini", + "BugReports": "https://github.com/dvdscripter/ini/issues", + "LazyData": "FALSE", + "RoxygenNote": "6.0.1", + "Suggests": [ + "testthat" + ], + "NeedsCompilation": "no", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "isoband": { + "Package": "isoband", + "Version": "0.3.0", + "Source": "Repository", + "Title": "Generate Isolines and Isobands from Regularly Spaced Elevation Grids", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Claus O.\", \"Wilke\", , \"wilke@austin.utexas.edu\", role = \"aut\", comment = c(\"Original author\", ORCID = \"0000-0002-7470-9261\")), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "A fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data.", + "License": "MIT + file LICENSE", + "URL": "https://isoband.r-lib.org, https://github.com/r-lib/isoband", + "BugReports": "https://github.com/r-lib/isoband/issues", + "Imports": [ + "cli", + "grid", + "rlang", + "utils" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "magick", + "bench", + "rmarkdown", + "sf", + "testthat (>= 3.0.0)", + "xml2" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-12-05", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "Config/build/compilation-database": "true", + "LinkingTo": [ + "cpp11" + ], + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut] (ORCID: ), Claus O. Wilke [aut] (Original author, ORCID: ), Thomas Lin Pedersen [aut, cre] (ORCID: ), Posit, PBC [cph, fnd] (ROR: )", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "RSPM" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository", + "Title": "Obtain 'jQuery' as an HTML Dependency Object", + "Authors@R": "c( person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@rstudio.com\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"), person(family = \"RStudio\", role = \"cph\"), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt\") )", + "Description": "Obtain any major version of 'jQuery' () and use it in any webpage generated by 'htmltools' (e.g. 'shiny', 'htmlwidgets', and 'rmarkdown'). Most R users don't need to use this package directly, but other R packages (e.g. 'shiny', 'rmarkdown', etc.) depend on this package to avoid bundling redundant copies of 'jQuery'.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Config/testthat/edition": "3", + "RoxygenNote": "7.0.2", + "Imports": [ + "htmltools" + ], + "Suggests": [ + "testthat" + ], + "NeedsCompilation": "no", + "Author": "Carson Sievert [aut, cre] (), Joe Cheng [aut], RStudio [cph], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/lib/jquery-AUTHORS.txt)", + "Maintainer": "Carson Sievert ", + "Repository": "RSPM" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "2.0.0", + "Source": "Repository", + "Title": "A Simple and Robust JSON Parser and Generator for R", + "License": "MIT + file LICENSE", + "Depends": [ + "methods" + ], + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Duncan\", \"Temple Lang\", role = \"ctb\"), person(\"Lloyd\", \"Hilaiel\", role = \"cph\", comment=\"author of bundled libyajl\"))", + "URL": "https://jeroen.r-universe.dev/jsonlite https://arxiv.org/abs/1403.2805", + "BugReports": "https://github.com/jeroen/jsonlite/issues", + "Maintainer": "Jeroen Ooms ", + "VignetteBuilder": "knitr, R.rsp", + "Description": "A reasonably fast JSON parser and generator, optimized for statistical data and the web. Offers simple, flexible tools for working with JSON in R, and is particularly powerful for building pipelines and interacting with a web API. The implementation is based on the mapping described in the vignette (Ooms, 2014). In addition to converting JSON data from/to R objects, 'jsonlite' contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.", + "Suggests": [ + "httr", + "vctrs", + "testthat", + "knitr", + "rmarkdown", + "R.rsp", + "sf" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Duncan Temple Lang [ctb], Lloyd Hilaiel [cph] (author of bundled libyajl)", + "Repository": "RSPM" + }, + "kableExtra": { + "Package": "kableExtra", + "Version": "1.4.0", + "Source": "Repository", + "Type": "Package", + "Title": "Construct Complex Table with 'kable' and Pipe Syntax", + "Authors@R": "c( person('Hao', 'Zhu', email = 'haozhu233@gmail.com', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-3386-6076')), person('Thomas', 'Travison', role = 'ctb'), person('Timothy', 'Tsai', role = 'ctb'), person('Will', 'Beasley', email = 'wibeasley@hotmail.com', role = 'ctb'), person('Yihui', 'Xie', email = 'xie@yihui.name', role = 'ctb'), person('GuangChuang', 'Yu', email = 'guangchuangyu@gmail.com', role = 'ctb'), person('Stéphane', 'Laurent', role = 'ctb'), person('Rob', 'Shepherd', role = 'ctb'), person('Yoni', 'Sidi', role = 'ctb'), person('Brian', 'Salzer', role = 'ctb'), person('George', 'Gui', role = 'ctb'), person('Yeliang', 'Fan', role = 'ctb'), person('Duncan', 'Murdoch', role = 'ctb'), person('Vincent', 'Arel-Bundock', role = 'ctb'), person('Bill', 'Evans', role = 'ctb') )", + "Description": "Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.", + "License": "MIT + file LICENSE", + "URL": "http://haozhu233.github.io/kableExtra/, https://github.com/haozhu233/kableExtra", + "BugReports": "https://github.com/haozhu233/kableExtra/issues", + "Depends": [ + "R (>= 3.1.0)" + ], + "Imports": [ + "knitr (>= 1.33)", + "magrittr", + "stringr (>= 1.0)", + "xml2 (>= 1.1.1)", + "rmarkdown (>= 1.6.0)", + "scales", + "viridisLite", + "stats", + "grDevices", + "htmltools", + "rstudioapi", + "tools", + "digest", + "graphics", + "svglite" + ], + "Suggests": [ + "testthat", + "magick", + "tinytex", + "formattable", + "sparkline", + "webshot2" + ], + "Config/testthat/edition": "3", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Language": "en-US", + "NeedsCompilation": "no", + "Author": "Hao Zhu [aut, cre] (), Thomas Travison [ctb], Timothy Tsai [ctb], Will Beasley [ctb], Yihui Xie [ctb], GuangChuang Yu [ctb], Stéphane Laurent [ctb], Rob Shepherd [ctb], Yoni Sidi [ctb], Brian Salzer [ctb], George Gui [ctb], Yeliang Fan [ctb], Duncan Murdoch [ctb], Vincent Arel-Bundock [ctb], Bill Evans [ctb]", + "Maintainer": "Hao Zhu ", + "Repository": "RSPM" + }, + "knitr": { + "Package": "knitr", + "Version": "1.51", + "Source": "Repository", + "Type": "Package", + "Title": "A General-Purpose Package for Dynamic Report Generation in R", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\", URL = \"https://yihui.org\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files 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person(\"Jeff\", \"Arnold\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", role = \"ctb\"), person(\"Jeremy\", \"Ashkenas\", role = c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), person(\"Rodrigo\", \"Copetti\", role = \"ctb\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Ruaridh\", \"Williamson\", role = \"ctb\"), person(\"Sagiru\", \"Mati\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1413-3974\")), person(\"Scott\", \"Kostyshak\", role = \"ctb\"), person(\"Sebastian\", \"Meyer\", role = \"ctb\"), person(\"Sietse\", \"Brouwer\", role = \"ctb\"), person(c(\"Simon\", \"de\"), \"Bernard\", role = \"ctb\"), person(\"Sylvain\", \"Rousseau\", role = \"ctb\"), person(\"Taiyun\", \"Wei\", role = \"ctb\"), person(\"Thibaut\", \"Assus\", role = \"ctb\"), person(\"Thibaut\", \"Lamadon\", role = \"ctb\"), person(\"Thomas\", \"Leeper\", role = \"ctb\"), person(\"Tim\", \"Mastny\", role = \"ctb\"), person(\"Tom\", \"Torsney-Weir\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = \"ctb\"), person(\"Viktoras\", 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an equivalent XPath expression. 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Supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT / STDERR over binary or text connections. 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This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. 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Also supports XML schema validation; for 'XSLT' transformations see the 'xslt' package.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org, https://r-lib.r-universe.dev/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "mockery", + "rmarkdown", + "testthat (>= 3.2.0)", + "xslt" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Jeroen Ooms [aut, cre], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Jeroen Ooms ", + "Repository": "RSPM" + }, + "xopen": { + "Package": "xopen", + "Version": "1.0.1", + "Source": "Repository", + "Title": "Open System Files, 'URLs', Anything", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Fathi\", \"Boudra\", role = \"aut\"), person(\"Rex\", \"Dieter\", role = \"aut\"), person(\"Kevin\", \"Krammer\", role = \"aut\"), person(\"Jeremy\", \"White\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Cross platform solution to open files, directories or 'URLs' with their associated programs.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/xopen#readme, https://r-lib.github.io/xopen/", + "BugReports": "https://github.com/r-lib/xopen/issues", + "Depends": [ + "R (>= 3.1)" + ], + "Imports": [ + "processx" + ], + "Suggests": [ + "ps", + "testthat (>= 3.0.0)" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Fathi Boudra [aut], Rex Dieter [aut], Kevin Krammer [aut], Jeremy White [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "RSPM", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]", + "Encoding": "UTF-8" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.12", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"cre\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Shawn\", \"Garbett\", , \"shawn.garbett@vumc.org\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4079-5621\")), person(\"Jeremy\", \"Stephens\", role = c(\"aut\", \"ctb\")), person(\"Kirill\", \"Simonov\", role = \"aut\"), person(\"Yihui\", \"Xie\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Zhuoer\", \"Dong\", role = \"ctb\"), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"reikoch\", role = \"ctb\"), person(\"Will\", \"Beasley\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5613-5006\")), person(\"Brendan\", \"O'Connor\", role = \"ctb\"), person(\"Michael\", \"Quinn\", role = \"ctb\"), person(\"Charlie\", \"Gao\", role = \"ctb\"), person(c(\"Gregory\", \"R.\"), \"Warnes\", role = \"ctb\"), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = \"ctb\") )", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://yaml.r-lib.org, https://github.com/r-lib/yaml/", + "BugReports": "https://github.com/r-lib/yaml/issues", + "Suggests": [ + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "VignetteBuilder": "knitr", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [cre] (ORCID: ), Shawn Garbett [ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" + }, + "zip": { + "Package": "zip", + "Version": "2.3.3", + "Source": "Repository", + "Title": "Cross-Platform 'zip' Compression", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", + "BugReports": "https://github.com/r-lib/zip/issues", + "Suggests": [ + "covr", + "pillar", + "processx", + "R6", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2025-05-07", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd] (ROR: )", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + } + } +} diff --git a/omicsdm-server/pipelines/snakemake/all/renv.lock b/omicsdm-server/pipelines/snakemake/bulk_sc/renv.lock_bk similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/renv.lock rename to omicsdm-server/pipelines/snakemake/bulk_sc/renv.lock_bk diff --git a/omicsdm-server/pipelines/snakemake/all/requirements.txt b/omicsdm-server/pipelines/snakemake/bulk_sc/requirements.txt similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/requirements.txt rename to omicsdm-server/pipelines/snakemake/bulk_sc/requirements.txt diff --git a/omicsdm-server/pipelines/snakemake/all/rules/renv.smk b/omicsdm-server/pipelines/snakemake/bulk_sc/rules/renv.smk similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/rules/renv.smk rename to omicsdm-server/pipelines/snakemake/bulk_sc/rules/renv.smk diff --git a/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess_new.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/data_preprocess.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess_new.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/data_preprocess.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/deseq2/deseq2.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/deseq2.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/deseq2/deseq2.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/deseq2.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/get_data_and_preprocess.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/deseq2/get_data_and_preprocess.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/get_data_and_preprocess.R diff --git a/omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/split_into_input_files.sh b/omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/split_into_input_files.sh new file mode 100644 index 0000000..d29bedb --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/src/deseq2/split_into_input_files.sh @@ -0,0 +1,53 @@ + +: ' +Split a combined metadata+counts CSV file into: + 1. INFO_*.csv → metadata (sample, Age, Gender, Group) + 2. COUNTS_*.csv → gene expression counts with genes as rows, samples as columns + +Input format (example): +"","Age","Gender","Group","EEF1A1","CD74" +"32150756",54,"Female","CTRL",182010.83,72 +"32150762",38,"Female","CTRL",269400.45,75 +... + +Steps: +- Extract sample metadata (first 4 columns) → INFO_*.csv +- Extract count matrix (sample IDs vs genes) → counts_wide_*.csv +- Transpose counts so it matches the by DESeq2 expected layout + (rows=genes, columns=samples) → COUNTS_*.csv + +Usage: + bash prepare_deseq2_input.sh all_samples.csv + +Dependencies: + - awk (POSIX) + - csvtk (https://bioinf.shenwei.me/csvtk/) for fast transpose +' + +IN="$1" +BASENAME=$(basename "$IN" .csv) + + +# 1. extract sample info (space-separated, strip quotes, prefix sample IDs with S_) +awk -F, 'BEGIN{OFS=" "} + NR==1 { $1="sample" } + { + for (i=1; i<=4; i++) gsub(/"/, "", $i) + if (NR>1) $1="S_" $1 + print $1,$2,$3,$4 + }' "$IN" > "INFO_${BASENAME}.csv" + +# 2. extract wide counts (samples as rows, genes as columns) +awk -F, 'BEGIN{OFS=","} + NR==1 { $1="\"gene_name\"" } + { + printf "%s",$1 + for (i=5;i<=NF;i++) printf "%s%s",OFS,$i + printf "\n" + }' "$IN" > counts_wide.csv + +# 3. transpose so genes are rows (DESeq2 style) +csvtk transpose -H counts_wide.csv | tr ',' ' ' > "COUNTS_${BASENAME}.csv" + +# clean up temporary file +rm counts_wide.csv \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea/fgsea.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea/fgsea.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/fgsea/fgsea.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea/fgsea.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea/get_data.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea/get_data.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/fgsea/get_data.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea/get_data.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea/reactome2gmt.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea/reactome2gmt.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/fgsea/reactome2gmt.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea/reactome2gmt.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/fgsea_wrapper.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea_wrapper.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/fgsea_wrapper.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/fgsea_wrapper.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/gsva/get_data.sh b/omicsdm-server/pipelines/snakemake/bulk_sc/src/gsva/get_data.sh similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/gsva/get_data.sh rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/gsva/get_data.sh diff --git a/omicsdm-server/pipelines/snakemake/all/src/gsva/sc_genesets_scoring_gsva.py b/omicsdm-server/pipelines/snakemake/bulk_sc/src/gsva/sc_genesets_scoring_gsva.py similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/gsva/sc_genesets_scoring_gsva.py rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/gsva/sc_genesets_scoring_gsva.py diff --git a/omicsdm-server/pipelines/snakemake/all/src/lib/build_report.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/lib/build_report.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/lib/build_report.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/lib/build_report.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/lib/install_renv.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/lib/install_renv.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/lib/install_renv.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/lib/install_renv.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/report/index.Rmd b/omicsdm-server/pipelines/snakemake/bulk_sc/src/report/index.Rmd similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/report/index.Rmd rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/report/index.Rmd diff --git a/omicsdm-server/pipelines/snakemake/all/src/report/libs.R b/omicsdm-server/pipelines/snakemake/bulk_sc/src/report/libs.R similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/report/libs.R rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/report/libs.R diff --git a/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/get_data.sh b/omicsdm-server/pipelines/snakemake/bulk_sc/src/sc_normalisation/get_data.sh similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/get_data.sh rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/sc_normalisation/get_data.sh diff --git a/omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/scRNA_normalisation.py b/omicsdm-server/pipelines/snakemake/bulk_sc/src/sc_normalisation/scRNA_normalisation.py similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/sc_normalisation/scRNA_normalisation.py rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/sc_normalisation/scRNA_normalisation.py diff --git a/omicsdm-server/pipelines/snakemake/all/src/z_scoring/get_data.sh b/omicsdm-server/pipelines/snakemake/bulk_sc/src/z_scoring/get_data.sh similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/z_scoring/get_data.sh rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/z_scoring/get_data.sh diff --git a/omicsdm-server/pipelines/snakemake/all/src/z_scoring/sc_genesets_z_scoring.py b/omicsdm-server/pipelines/snakemake/bulk_sc/src/z_scoring/sc_genesets_z_scoring.py similarity index 100% rename from omicsdm-server/pipelines/snakemake/all/src/z_scoring/sc_genesets_z_scoring.py rename to omicsdm-server/pipelines/snakemake/bulk_sc/src/z_scoring/sc_genesets_z_scoring.py diff --git a/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json b/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json index 96fd181..a42837e 100644 --- a/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json +++ b/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json @@ -1,14 +1,20 @@ { + "bases_on": null, + "control": "CTRL", + "contrast": { + "SLE_vs_CTRL": "Group,SLE,CTRL" + }, "files": [ - "3tr/test/COUNTS_genes_TEST_134_135_summed.csv_uploadedVersion_1.csv", - "3tr/test/info_TEST_134_135.csv_uploadedVersion_1.csv" + "in/INFO_Bcells_bulkRNAseq.csv", + "in/COUNTS_Bcells_bulkRNAseq.csv" ], - "options": { - "profiling": "TRUE", - "onlypca": "FALSE", - "plot": "TRUE", - "project": "TEST_134_135", - "control": "TEST_134_500", - "bases_on": null - } + "filetype_to_filename": { + "info": "INFO_Bcells_bulkRNAseq.csv", + "counts": "COUNTS_Bcells_bulkRNAseq.csv" + }, + "onlypca": "FALSE", + "profiling": "TRUE", + "plot": "TRUE", + "plot_atr": { "de_genes_n": 50, "heatmap_ann": "Group", "pca": "Group" }, + "project": "bulkRNAseq_base_analysis" } diff --git a/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R b/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R index c3ba92f..14857bb 100644 --- a/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R +++ b/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R @@ -14,44 +14,44 @@ print("---R-logs---") print("start deseq2.R") print("start loading libs") -library("jsonlite", character.only = TRUE) -library("stringr", character.only = TRUE) -library("glue", character.only = TRUE) -library("DESeq2", character.only = TRUE) -library("BiocParallel", character.only = TRUE) -library("pheatmap", character.only = TRUE) -library("RColorBrewer", character.only = TRUE) -library("ggplot2", character.only = TRUE) -library("genefilter", character.only = TRUE) -library("gridExtra", character.only = TRUE) -library("grid", character.only = TRUE) -library("methods", character.only = TRUE) -library("tibble", character.only = TRUE) -library("dplyr", character.only = TRUE) -library("openxlsx", character.only = TRUE) - -libs <- c( - "jsonlite", - "stringr", - "glue", - "DESeq2", - "BiocParallel", - "pheatmap", - "RColorBrewer", - "ggplot2", - "genefilter", - "gridExtra", - "grid", - "methods", - "tibble", - "dplyr", - "openxlsx" -) -for (lib in libs) { - print(lib) - suppressPackageStartupMessages(library(lib, character.only = TRUE)) -} -print("libs loaded") +library("jsonlite") +library("stringr") +library("glue") +library("DESeq2") +library("BiocParallel") +library("pheatmap") +library("RColorBrewer") +library("ggplot2") +library("genefilter") +library("gridExtra") +library("grid") +library("methods") +library("tibble") +library("dplyr") +library("openxlsx") + +# libs <- c( +# "jsonlite", +# "stringr", +# "glue", +# "DESeq2", +# "BiocParallel", +# "pheatmap", +# "RColorBrewer", +# "ggplot2", +# "genefilter", +# "gridExtra", +# "grid", +# "methods", +# "tibble", +# "dplyr", +# "openxlsx" +# ) +# for (lib in libs) { +# print(lib) +# suppressPackageStartupMessages(library(lib, character.only = TRUE)) +# } +# print("libs loaded") getEnv_fromJSON <- function(json) { cat("getEnv_fromJSON", json) @@ -121,9 +121,11 @@ getEnv_fromObj <- function(cfg) { # read in json passed from omicsdm_server -script_options <- fromJSON("analysis_options.json") +script_options <- fromJSON("config/deseq2.json") +print("got script_options from deseq2.json") +print(script_options) script_options$project <- "bulkRNAseq_base_analysis" -project <- paste("out/results/", script_options$project, sep = "") +project <- paste("out/results/deseq2/", script_options$project, sep = "") # control <- script_options$control control <- "CTRL" group <- script_options$group @@ -161,6 +163,16 @@ getEnv_fromObj(cfg_obj) counts_raw <- readRDS("out/rds/deseq2_obj1.rds") info_raw <- readRDS("out/rds/deseq2_obj2.rds") +print("counts_raw") +print(head(counts_raw)) +print("colnames(counts_raw)") +print(colnames(counts_raw)) + +print("info_raw") +print(head(info_raw)) +print("row.names(info_raw)") +print(row.names(info_raw)) + # make sure that the counts are integer cols <- names(counts_raw)[2:dim(counts_raw)[2]] counts_raw[cols] <- lapply(counts_raw[cols], as.integer) @@ -266,6 +278,9 @@ colnames(colData(dds)) dds[[group]] <- relevel(dds[[group]], control) print("after relevel control group") +print ("onlypca") +print (onlypca) + ## DIFFERENTIAL ANALYSIS ## # print("sessionInfo") @@ -311,6 +326,8 @@ if ((plot)) { row.names = row.names(colData(dds)) ) print("after annotation_heatmap as.data.frame") + print("annotation_heatmap") + print(head(annotation_heatmap)) names(annotation_heatmap) <- plot_atr$heatmap_ann ## SAVED: annotation_col = as.data.frame(coldata[,plot_atr$heatmap_ann] @@ -472,14 +489,21 @@ process_contrast <- function(title, contrastos) { contrast = contrastos, parallel = FALSE ) + res2 <- lfcShrink(dds, contrast = contrastos, res = resAll, type = "normal") + print("head res2") + print(head(res2)) + res <- subset(res2, abs(log2FoldChange) > log2(1.5)) + + resOrdered <- res[order(res$padj), ] resAllOrdered <- resAll[order(resAll$padj), ] ## EXTRACT COUNTS NORMALIZED ## c <- counts(dds, normalized = TRUE) c_ordered <- c[rownames(resAllOrdered), ] + colnames(c_ordered) <- paste( dds[[contrastos[1]]], ",", @@ -487,6 +511,7 @@ process_contrast <- function(title, contrastos) { sep = "" ) counts_dds <- (c_ordered[, order(colnames(c_ordered))]) + cc <- round(counts_dds, digits = 2) ## EXTRACT DESCRIPTION AND SUMMARY ## @@ -512,8 +537,18 @@ process_contrast <- function(title, contrastos) { ) df_all <- as.data.frame(resAllOrdered) + + print("df_all before adding columns") + print(head(df_all)) + # print("rownames(df_all)") + # print(rownames(df_all)) + df_all["filter"] <- pass_filter df_all["shrunkenlfc"] <- res2[rownames(df_all), "log2FoldChange"] + + print("df_all after adding columns") + print(head(df_all)) + df_all <- df_all[, c( "baseMean", "log2FoldChange", @@ -603,7 +638,7 @@ if (!onlypca) { sink(format( Sys.time(), - glue("out/results/sessionInfo/sessionInfo.txt") + glue("out/results/deseq2/sessionInfo/sessionInfo.txt") )) print(devtools::session_info()) sink() @@ -619,5 +654,5 @@ packages_df <- devtools::session_info()$packages %>% dplyr::select(loadedversion, date, source) %>% rownames_to_column() -saveRDS(platform_df, "out/results/sessionInfo/platform.rds") -saveRDS(packages_df, "out/results/sessionInfo/packages.rds") +saveRDS(platform_df, "out/results/deseq2/sessionInfo/platform.rds") +saveRDS(packages_df, "out/results/deseq2/sessionInfo/packages.rds") \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/deseq2/src/get_data_and_preprocess_new.R b/omicsdm-server/pipelines/snakemake/deseq2/src/get_data_and_preprocess_new.R index 540efc5..faea759 100644 --- a/omicsdm-server/pipelines/snakemake/deseq2/src/get_data_and_preprocess_new.R +++ b/omicsdm-server/pipelines/snakemake/deseq2/src/get_data_and_preprocess_new.R @@ -1,25 +1,12 @@ print("---R-logs---") -print("start get_data_and_preprocess.R") +print("start data_preprocess.R") print("start loading libs") -libs <- c("httr", "dplyr", "stringr", "jsonlite", "paws") -for (lib in libs) { - print(lib) - suppressPackageStartupMessages(library(lib, character.only = TRUE)) -} -print("libs loaded") -# https://github.com/Bioconductor/GenomicDataCommons/issues/35#issuecomment-284096739 -# set_config(config(ssl_verifypeer = 0L, ssl_verifyhost = 0L, verbose = F)) -set_config(httr::config(ssl_verifypeer = 0L, ssl_verifyhost = 0L, verbose = F)) +library("dplyr") +library("jsonlite") -# set_config(config(cainfo="/home/certs/vm2rootCA.pem",verbose=T)) - -# might be that it is not able to find the .Renviron file -readRenviron(".Renviron") -bucket <- Sys.getenv("BUCKET_NAME") - -script_options <- fromJSON("analysis_options.json") -file_paths <- script_options$file_paths +script_options <- fromJSON("config/deseq2.json") +file_paths <- script_options$files filetype_to_filename <- script_options$filetype_to_filename # get the filename of the count file @@ -31,34 +18,17 @@ info_filepath <- file_paths[grep(info_filename, file_paths)] print(paste0("counts_filepath: ", counts_filepath)) print(paste0("info_filepath: ", info_filepath)) -s3 <- paws::s3( - config = list( - credentials = list( - creds = list( - access_key_id = "admin", - secret_access_key = "12345678" - ) - ), - endpoint = "https://minio.omicsdm.cnag.dev", - s3_force_path_style = TRUE, - region = "us-east-1" - ) +counts_tbl <- read.csv( + counts_filepath, + sep=" " ) -print("start get_object") - -counts_obj <- s3$get_object(Bucket = bucket, Key = counts_filepath) -counts_tbl <- read.csv(text = rawToChar(counts_obj$Body), sep=" ") - -# Anna Esteve -# counts_tbl <- read.csv(text = rawToChar(counts_obj$Body)) print("got counts file") -info_obj <- s3$get_object(Bucket = bucket, Key = info_filepath) -info_tbl <- read.csv(text = rawToChar(info_obj$Body), sep=" ") - -# Anna Esteve -# info_tbl <- read.csv(text = rawToChar(info_obj$Body)) +info_tbl <- read.csv( + info_filepath, + sep=" " +) print("got info file") @@ -78,13 +48,14 @@ counts_df <- tidyr::separate( into = new_colnames, remove = TRUE ) -# counts_df <- counts_tbl -# rownames(counts_df) <- counts_df$id_gene -# counts_df$id_gene <- NULL counts_df <- counts_tbl -rownames(counts_df) <- counts_df$gene_id -counts_df$gene_id <- NULL +rownames(counts_df) <- counts_df$gene_name +counts_df$gene_name <- NULL + +# round numeric columns in the counts_df +is.num <- sapply(counts_df, is.numeric) +counts_df[is.num] <- lapply(counts_df[is.num], round) new_colnames <- unlist(strsplit(colnames(info_tbl)[1], "[.]")) info_df <- tidyr::separate( @@ -95,35 +66,24 @@ info_df <- tidyr::separate( remove = TRUE ) info_df <- info_tbl -colnames(info_df) <- toupper(colnames(info_df)) -# drop the columns AGE and GENDER if they exist -if ("AGE" %in% colnames(info_df)) { - info_df$AGE <- NULL -} -if ("GENDER" %in% colnames(info_df)) { - info_df$GENDER <- NULL -} - -# fix the typo in the example file from Anna Esteve -# rownames(info_df) <- info_df$BARCDODE -# info_df$BARCDODE <- NULL - -rownames(info_df) <- info_df$BARCODE -info_df$BARCODE <- NULL - -print("resource1") -head(counts_df) -print("resource2") -head(info_df) -saveRDS(counts_df, "out/rds/deseq2_obj1.rds") -saveRDS(info_df, "out/rds/deseq2_obj2.rds") +rownames(info_df) <- info_df$sample +info_df$sample <- NULL + +print("colnames(info_df)") +print(colnames(info_df)) -# rownames(info_tbl) <- info_tbl$BARCDODE -# info_tbl$BARCDODE <- NULL +# Scale/factor variables +info_df$Age <- scale(info_df$Age, center = TRUE, scale = TRUE) +info_df$Gender <- as.factor(info_df$Gender) +info_df$Group <- as.factor(info_df$Group) -# print(head(counts_tbl)) -# print(head(info_tbl)) +# verify factor levels +print("levels(info_df$Gender)") +print(levels(info_df$Gender)) -# saveRDS(counts_tbl, "out/rds/deseq2_obj1.rds") -# saveRDS(info_tbl, "out/rds/deseq2_obj2.rds") \ No newline at end of file +print("levels(info_df$Group)") +print(levels(info_df$Group)) + +saveRDS(counts_df, "out/rds/deseq2_obj1.rds") +saveRDS(info_df, "out/rds/deseq2_obj2.rds") \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R b/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R index b29b9b4..3290cec 100644 --- a/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R +++ b/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R @@ -2,19 +2,28 @@ print("---R-logs---") print("start fgsea.R") print("start loading libs") -libs <- c( - "fgsea", - "data.table", - "glue", - "dplyr", - "tibble", - "BiocParallel", - "jsonlite" -) -for (lib in libs) { - print(lib) - suppressPackageStartupMessages(library(lib, character.only = TRUE)) -} + +library("fgsea") +library("data.table") +library("glue") +library("dplyr") +library("tibble") +library("BiocParallel") +library("jsonlite") + +# libs <- c( +# "fgsea", +# "data.table", +# "glue", +# "dplyr", +# "tibble", +# "BiocParallel", +# "jsonlite" +# ) +# for (lib in libs) { +# print(lib) +# suppressPackageStartupMessages(library(lib, character.only = TRUE)) +# } print("libs loaded") ### Parse args From 4a215e6ad10871b70dd94e7e789bcc1383f753ee Mon Sep 17 00:00:00 2001 From: Ivo Leist Date: Fri, 6 Feb 2026 06:52:34 +0100 Subject: [PATCH 6/6] started to make fgsea work again --- .../pipelines/snakemake/bulk_sc/Snakefile | 57 +++++++------------ .../pipelines/snakemake/bulk_sc/src/README.md | 8 +++ .../snakemake/deseq2/config/deseq2.json | 2 +- .../pipelines/snakemake/deseq2/src/deseq2.R | 2 +- .../snakemake/fgsea/config/fgsea.json | 16 ++---- .../pipelines/snakemake/fgsea/src/fgsea.R | 2 +- 6 files changed, 36 insertions(+), 51 deletions(-) create mode 100644 omicsdm-server/pipelines/snakemake/bulk_sc/src/README.md diff --git a/omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile b/omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile index d8fa915..5a5ec0b 100644 --- a/omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/Snakefile @@ -14,8 +14,8 @@ rule all: rule report: input: # Outputs from all pipelines - deseq2_results="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", - # fgsea_results="out/results/fgsea/significant_genesets.gmt", + deseq2_results="out/results/deseq2/bulkRNAseq_deseq2_SLE_vs_CTRL_results.txt", + fgsea_results="out/results/fgsea/_fgsea.pdf", # sc_norm_results="out/results/sc_normalisation/normalised.h5ad", # z_scoring_results="out/results/z_scoring/z-scored.h5ad", # gsva_results="out/results/gsva/gsva-scored.h5ad", @@ -55,8 +55,8 @@ rule deseq2_analysis: rds_obj2="out/rds/deseq2_obj2.rds", config="config/deseq2.json", output: - out3="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", - out5="out/results/deseq2/sessionInfo/sessionInfo.txt", + out="out/results/deseq2/bulkRNAseq_deseq2_SLE_vs_CTRL_results.txt", + R_session_info="out/results/deseq2/sessionInfo/sessionInfo.txt", log: "log/deseq2_analysis.log", shell: @@ -66,40 +66,21 @@ rule deseq2_analysis: """ # 2. FGSEA Analysis (depends on DESeq2 output) -# rule fgsea_analysis: -# input: -# in1="in/fgsea/results.tar.gz", -# in2="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", -# config="config/fgsea.json", -# # Ensure DESeq2 completes first -# deseq2_done="out/results/deseq2/bulkRNAseq_base_analysis_rlogMat.txt", -# output: -# out7="out/results/fgsea/sessionInfo/sessionInfo.txt", -# out8="out/results/fgsea/sessionInfo/platform.rds", -# out9="out/results/fgsea/sessionInfo/packages.rds", -# significant_genesets="out/results/fgsea/significant_genesets.gmt", -# log: -# "log/fgsea_analysis.log", -# shell: -# """ -# mkdir -p out/results/fgsea/sessionInfo -# {runR} src/fgsea_wrapper.R | tee {log} -# """ - - -# rule fgsea_get_data: -# input: -# config="config/fgsea.json", -# output: -# out1="in/fgsea/results.tar.gz", -# out4="out/tmp/c6.all.v2023.2.Hs.symbols.gmt", -# log: -# "log/fgsea_get_data.log", -# shell: -# """ -# mkdir -p in/fgsea out/tmp -# {runR} src/fgsea/get_data.R {input.config} | tee {log} -# """ +rule fgsea_analysis: + input: + config="config/fgsea.json", + deseq2_out="out/results/deseq2/bulkRNAseq_deseq2_SLE_vs_CTRL_results.txt", + gmt="in/c6.all.v2023.2.Hs.symbols.gmt", + output: + out="out/results/fgsea/_fgsea.pdf", + R_session_info="out/results/fgsea/sessionInfo/sessionInfo.txt", + log: + "log/fgsea_analysis.log", + shell: + """ + mkdir -p out/results/fgsea/sessionInfo + {runR} src/fgsea_wrapper.R | tee {log} + """ # # --- Single-cell RNA-seq Pipeline --- # diff --git a/omicsdm-server/pipelines/snakemake/bulk_sc/src/README.md b/omicsdm-server/pipelines/snakemake/bulk_sc/src/README.md new file mode 100644 index 0000000..1ca0824 --- /dev/null +++ b/omicsdm-server/pipelines/snakemake/bulk_sc/src/README.md @@ -0,0 +1,8 @@ +The files in here are symbolic links to the actual source files. +So modifications in here modify the actual source files. + +Thus, before merging these changes (with the main branch) +copy the modified files to an extra folder so the scripts +inside the folders inside +pipelines/snakemake are not overwritten ! + diff --git a/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json b/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json index a42837e..4c7f7a9 100644 --- a/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json +++ b/omicsdm-server/pipelines/snakemake/deseq2/config/deseq2.json @@ -16,5 +16,5 @@ "profiling": "TRUE", "plot": "TRUE", "plot_atr": { "de_genes_n": 50, "heatmap_ann": "Group", "pca": "Group" }, - "project": "bulkRNAseq_base_analysis" + "project": "bulkRNAseq_deseq2" } diff --git a/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R b/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R index 14857bb..294c884 100644 --- a/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R +++ b/omicsdm-server/pipelines/snakemake/deseq2/src/deseq2.R @@ -124,7 +124,7 @@ getEnv_fromObj <- function(cfg) { script_options <- fromJSON("config/deseq2.json") print("got script_options from deseq2.json") print(script_options) -script_options$project <- "bulkRNAseq_base_analysis" +# script_options$project <- "bulkRNAseq_base_analysis" project <- paste("out/results/deseq2/", script_options$project, sep = "") # control <- script_options$control control <- "CTRL" diff --git a/omicsdm-server/pipelines/snakemake/fgsea/config/fgsea.json b/omicsdm-server/pipelines/snakemake/fgsea/config/fgsea.json index 96fd181..14048ef 100644 --- a/omicsdm-server/pipelines/snakemake/fgsea/config/fgsea.json +++ b/omicsdm-server/pipelines/snakemake/fgsea/config/fgsea.json @@ -1,14 +1,10 @@ { - "files": [ - "3tr/test/COUNTS_genes_TEST_134_135_summed.csv_uploadedVersion_1.csv", - "3tr/test/info_TEST_134_135.csv_uploadedVersion_1.csv" - ], + "files": { + "gmt": "c6.all.v2023.2.Hs.symbols.gmt" + }, "options": { "profiling": "TRUE", - "onlypca": "FALSE", - "plot": "TRUE", - "project": "TEST_134_135", - "control": "TEST_134_500", - "bases_on": null + "bases_on": "deseq2", + "use_reactome_identifier_mapping_file": null } -} +} \ No newline at end of file diff --git a/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R b/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R index 3290cec..4e64135 100644 --- a/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R +++ b/omicsdm-server/pipelines/snakemake/fgsea/src/fgsea.R @@ -146,7 +146,7 @@ out_dir <- "out/results" files <- Sys.glob(file.path(in_dir, "*results.txt")) # read in json passed from omicsdm_server -script_options <- fromJSON("analysis_options.json") +script_options <- fromJSON("config/fgsea.json") print(script_options) reactome_identifier_mapping_file <- script_options$use_reactome_identifier_mapping_file