Tal ciona atlas backup

.gitignore

@@ -10,14 +10,17 @@ Scully_mannitol_2025/scRNA-seq_python_scripts/raw_unfiltered_data/*
 # Large files to exclude in Scully et al. Ciona atlas
 Scully_Ciona_blood_2025/data/*
 !Scully_Ciona_blood_2025/data/README.md
-Scully_Ciona_blood_2025/scRNA-seq_analysis/go_enrichment_analysis/go_enrichment_analysis_output/*
 Scully_Ciona_blood_2025/scRNA-seq_analysis/gene_enrichment_analysis/curated_gene_sets_fishers_output/*
 Scully_Ciona_blood_2025/scRNA-seq_analysis/gene_enrichment_analysis/curated_gene_sets_gsea_output/*
 Scully_Ciona_blood_2025/scRNA-seq_analysis/gene_enrichment_analysis/kegg_pathway_fishers_output/*
 Scully_Ciona_blood_2025/scRNA-seq_analysis/gene_enrichment_analysis/kegg_pathway_gsea_output/*
 Scully_Ciona_blood_2025/scRNA-seq_analysis/differentiation_hierarchy_analysis/differentiation_graph_output/*
 Scully_Ciona_blood_2025/species_comparisons/gs_plots/gs_plots_Hs_vs_Cr_output/*
 Scully_Ciona_blood_2025/species_comparisons/gs_plots/gs_plots_Hs_vs_Dr_output/*
+Scully_Ciona_blood_2025/species_comparisons/coexpression_conservation/coexpr_cons_Hs_vs_Cr_output/*
+Scully_Ciona_blood_2025/species_comparisons/coexpression_conservation/coexpr_cons_Hs_vs_Dr_output/*
+Scully_Ciona_blood_2025/species_comparisons/coexpression_conservation/tf_coexpr_Hs_vs_Cr_output/*
+Scully_Ciona_blood_2025/species_comparisons/coexpression_conservation/tf_coexpr_Hs_vs_Dr_output/*
 Scully_Ciona_blood_2025/HCR_FISH/napari_image_analysis_pipeline/raw_images/*
 !Scully_Ciona_blood_2025/HCR_FISH/napari_image_analysis_pipeline/raw_images/SAMPLE_INFO.csv
 Scully_Ciona_blood_2025/HCR_FISH/napari_image_analysis_pipeline/image_analysis_pipeline_output/*

Scully_Ciona_blood_2025/HCR_FISH/napari_image_analysis_pipeline/README.md

@@ -2,7 +2,7 @@ The scripts in this folder were used to analyze images for HCR FISH, specificall
 
 Key files in this folder:
 - `image_analysis_pipeline.py` runs the image analysis pipeline. This readme describes how to run it, and what file structure it expects for raw image files.
-- `napari_image_analysis_env.txt` contains information on the conda environment used, saved to a text file (by running `conda list --explicit > napari_image_analysis_env.txt`).
+- `napari_image_analysis_env.yml` and `napari_image_analysis_env.txt` contain information on the conda environment used, saved to a text file (by running `conda env export --no-builds > napari_image_analysis_env.yml` and `conda list --explicit > napari_image_analysis_env.txt`). The .txt files is for MacOS only.
 - `raw_images/` is a folder which must contain the raw imaging files to successfully run `image_analysis_pipeline.py`. See "[Subfolder structure](#subfolder-structure)" for more detail.
 - `HCR_PROBES_MASTER_LIST.xlsx` is an excel spreadsheet containing a conversion between probe IDs used in python scripts (e.g. HP14) and genes labeled (e.g. KY21.Chr11.687). This is needed to run `image_analysis_pipeline.py`.
 

Scully_Ciona_blood_2025/HCR_FISH/napari_image_analysis_pipeline/napari_image_analysis_env.yml

@@ -0,0 +1,187 @@
+name: napari-env
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - bzip2=1.0.8
+  - ca-certificates=2021.10.8
+  - libffi=3.4.2
+  - libzlib=1.2.11
+  - ncurses=6.3
+  - openssl=3.0.0
+  - pip=22.0.4
+  - python=3.9.10
+  - python_abi=3.9
+  - readline=8.1
+  - setuptools=60.9.3
+  - sqlite=3.37.0
+  - tk=8.6.12
+  - tzdata=2021e
+  - wheel=0.37.1
+  - xz=5.2.5
+  - zlib=1.2.11
+  - pip:
+      - absl-py==1.4.0
+      - alabaster==0.7.12
+      - appdirs==1.4.4
+      - appnope==0.1.2
+      - asttokens==2.0.5
+      - astunparse==1.6.3
+      - attrs==21.4.0
+      - babel==2.9.1
+      - backcall==0.2.0
+      - cachetools==5.3.0
+      - cachey==0.2.1
+      - certifi==2021.10.8
+      - charset-normalizer==2.0.12
+      - click==8.0.4
+      - cloudpickle==2.0.0
+      - contourpy==1.0.7
+      - csbdeep==0.7.3
+      - cycler==0.11.0
+      - dask==2022.2.1
+      - debugpy==1.5.1
+      - decorator==5.1.1
+      - docstring-parser==0.13
+      - docutils==0.17.1
+      - entrypoints==0.4
+      - et-xmlfile==1.1.0
+      - executing==0.8.3
+      - flatbuffers==23.3.3
+      - fonttools==4.38.0
+      - freetype-py==2.2.0
+      - fsspec==2022.2.0
+      - gast==0.4.0
+      - google-auth==2.17.0
+      - google-auth-oauthlib==0.4.6
+      - google-pasta==0.2.0
+      - grpcio==1.53.0
+      - h5py==3.8.0
+      - heapdict==1.0.1
+      - hsluv==5.0.2
+      - idna==3.3
+      - imagecodecs==2023.3.16
+      - imageio==2.16.1
+      - imagesize==1.3.0
+      - imglyb==2.0.1
+      - importlib-metadata==4.11.2
+      - intervaltree==3.1.0
+      - ipykernel==6.9.1
+      - ipython==8.1.1
+      - ipython-genutils==0.2.0
+      - jax==0.4.8
+      - jedi==0.18.1
+      - jgo==1.0.5
+      - jinja2==3.0.3
+      - joblib==1.2.0
+      - jpype1==1.4.1
+      - jsonschema==4.4.0
+      - jupyter-client==7.1.2
+      - jupyter-core==4.9.2
+      - keras==2.12.0
+      - kiwisolver==1.3.2
+      - labeling==0.1.13
+      - libclang==16.0.0
+      - llvmlite==0.39.1
+      - locket==0.2.1
+      - magicgui==0.3.7
+      - markdown==3.4.3
+      - markupsafe==2.1.2
+      - matplotlib==3.6.3
+      - matplotlib-inline==0.1.3
+      - matplotlib-scalebar==0.8.1
+      - ml-dtypes==0.0.4
+      - napari==0.4.14
+      - napari-console==0.0.4
+      - napari-plugin-engine==0.2.0
+      - napari-svg==0.1.6
+      - nd2==0.5.3
+      - nd2reader==3.3.0
+      - nest-asyncio==1.5.4
+      - networkx==2.7.1
+      - npe2==0.1.2
+      - numba==0.56.4
+      - numpy==1.22.3
+      - numpydoc==1.2
+      - oauthlib==3.2.2
+      - openpyxl==3.1.2
+      - opt-einsum==3.3.0
+      - packaging==21.3
+      - pandas==1.4.1
+      - parso==0.8.3
+      - partd==1.2.0
+      - pexpect==4.8.0
+      - pickleshare==0.7.5
+      - pillow==9.0.1
+      - pims==0.6.1
+      - pint==0.18
+      - pooch==1.6.0
+      - prompt-toolkit==3.0.28
+      - protobuf==4.22.1
+      - psutil==5.9.0
+      - psygnal==0.3.3
+      - ptyprocess==0.7.0
+      - pure-eval==0.2.2
+      - pyasn1==0.4.8
+      - pyasn1-modules==0.2.8
+      - pydantic==1.9.0
+      - pygments==2.11.2
+      - pyopengl==3.1.6
+      - pyparsing==3.0.7
+      - pyqt5==5.15.6
+      - pyqt5-qt5==5.15.2
+      - pyqt5-sip==12.9.1
+      - pyrsistent==0.18.1
+      - python-dateutil==2.8.2
+      - pytomlpp==1.0.10
+      - pytz==2021.3
+      - pywavelets==1.2.0
+      - pyyaml==6.0
+      - pyzmq==22.3.0
+      - qtconsole==5.2.2
+      - qtpy==2.0.1
+      - requests==2.27.1
+      - requests-oauthlib==1.3.1
+      - resource-backed-dask-array==0.1.0
+      - rsa==4.9
+      - scikit-image==0.19.2
+      - scikit-learn==1.2.1
+      - scipy==1.8.0
+      - scyjava==1.8.1
+      - seaborn==0.12.2
+      - six==1.16.0
+      - slicerator==1.1.0
+      - snowballstemmer==2.2.0
+      - sortedcontainers==2.4.0
+      - sphinx==4.4.0
+      - sphinxcontrib-applehelp==1.0.2
+      - sphinxcontrib-devhelp==1.0.2
+      - sphinxcontrib-htmlhelp==2.0.0
+      - sphinxcontrib-jsmath==1.0.1
+      - sphinxcontrib-qthelp==1.0.3
+      - sphinxcontrib-serializinghtml==1.1.5
+      - stack-data==0.2.0
+      - superqt==0.3.1
+      - tensorboard==2.12.0
+      - tensorboard-data-server==0.7.0
+      - tensorboard-plugin-wit==1.8.1
+      - tensorflow-estimator==2.12.0
+      - tensorflow-io-gcs-filesystem==0.32.0
+      - termcolor==2.2.0
+      - threadpoolctl==3.1.0
+      - tifffile==2022.2.9
+      - toolz==0.11.2
+      - tornado==6.1
+      - tqdm==4.63.0
+      - traitlets==5.1.1
+      - typer==0.4.0
+      - typing-extensions==4.1.1
+      - urllib3==1.26.8
+      - vispy==0.9.6
+      - wcwidth==0.2.5
+      - werkzeug==2.2.3
+      - wrapt==1.13.3
+      - xarray==2023.2.0
+      - xmltodict==0.13.0
+      - zipp==3.7.0

Scully_Ciona_blood_2025/README.md

@@ -26,3 +26,4 @@ Contains several helper function files used in scripts throughout the folder.
 
 ### Subfolder `cross_species_comparisons/`
 - `gs_plots/` contains scripts for making generalized Sankey (GS) plots and calculating Jaccard similarity scores.
+- `coexpression_conservation/` contains scripts for quantifying gene coexpression conservation.

Scully_Ciona_blood_2025/helper_functions/gillis_style_coexpression_hf.py

@@ -9,8 +9,6 @@
 
 # Change this path to point to folder containing gene_hf.py
 # This imports dictionaries and functions for easily converting gene ids
-path_to_dropbox = os.environ['PATH_TO_DROPBOX']
-sys.path.append(path_to_dropbox + 'klein_lab/resources/helper_functions')
 import scrna_helper_functions as hf
 
 # ============================================================================

Scully_Ciona_blood_2025/scRNA-seq_analysis/differentiation_hierarchy_analysis/README.md

@@ -2,4 +2,4 @@ The scripts in this folder were used to generate a hypothesized hematopoietic hi
 
 The files are:
 - `differentiation_graph.py` is the python script that uses the scRNA-seq data to generate a hypothesized hierarchy. The script outputs a folder `differentiation_graph_output/` containing plots of the inferred hierarchy (graph, adjacency matrix), a text file listing cell states not connected to other nodes in the graph, as well as miscellaneous supporting plots.
-- `differentiation_graph_env.txt` contains information on the conda environment used, saved to a text file (by running `conda list --explicit > differentiation_graph_env.txt`).
+- `differentiation_graph_env.yml` and `differentiation_graph_env.txt` contain information on the conda environment used, saved to a text file (by running `conda env export --no-builds > differentiation_graph_env.yml` and `conda list --explicit > differentiation_graph_env.txt`). The .txt files is for MacOS only.