From 63c0945361b133574d31b524734ce9b1f9322f28 Mon Sep 17 00:00:00 2001 From: "Abolfazl (Abe)" Date: Mon, 28 Aug 2023 21:26:31 -0700 Subject: [PATCH 1/7] add `suppressMessages` --- src/_R/DESeq.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/_R/DESeq.R b/src/_R/DESeq.R index 245aa30..c03097b 100644 --- a/src/_R/DESeq.R +++ b/src/_R/DESeq.R @@ -1,6 +1,6 @@ -library(DESeq2) -library(gplots) -library(tibble) +suppressMessages(suppressWarnings(library (DESeq2))) +suppressMessages(suppressWarnings(library (gplots))) +suppressMessages(suppressWarnings(library (tibble))) args <- commandArgs(trailingOnly = TRUE) From 6653d9d0dfd88ddf93582f1e2dbe0d09cd21306e Mon Sep 17 00:00:00 2001 From: "Abolfazl (Abe)" Date: Mon, 28 Aug 2023 21:30:14 -0700 Subject: [PATCH 2/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5d26b9d..41c9cb8 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ REMBRANDTS is a package for analysis of RNA-seq data across multiple samples in 1. Unix-compatible OS 2. [R](https://www.r-project.org/) version 3.2.3 or later 3. R [gplots](https://cran.r-project.org/web/packages/gplots/index.html) library -4. R [DESeq](http://bioconductor.org/packages/release/bioc/html/DESeq.html) library +4. R [DEseq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) library (previously [DESeq](http://bioconductor.org/packages/release/bioc/html/DESeq.html)) ### Installation From 8da5d4b87be96bf1328106fbf8ff783ca7da7c8d Mon Sep 17 00:00:00 2001 From: abearab Date: Mon, 28 Aug 2023 21:41:36 -0700 Subject: [PATCH 3/7] add `environment` file --- environment.yml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 environment.yml diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..88dbb1e --- /dev/null +++ b/environment.yml @@ -0,0 +1,9 @@ +name: stbl +channels: + - conda-forge + - bioconda +dependencies: + - bioconductor-deseq2 + - gplots + - tibble + - ipykernel \ No newline at end of file From abb6664980fcd7d2283c54392d1bcfa432874699 Mon Sep 17 00:00:00 2001 From: abearab Date: Mon, 28 Aug 2023 21:43:55 -0700 Subject: [PATCH 4/7] update names --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index 88dbb1e..1f7511c 100644 --- a/environment.yml +++ b/environment.yml @@ -4,6 +4,6 @@ channels: - bioconda dependencies: - bioconductor-deseq2 - - gplots - - tibble - - ipykernel \ No newline at end of file + - r-gplots + - r-tibble + - ipykernel From 8c9614ba75cb50e1697067835252b81d778e2446 Mon Sep 17 00:00:00 2001 From: abearab Date: Mon, 28 Aug 2023 21:53:15 -0700 Subject: [PATCH 5/7] add `suppressMessages` --- src/_R/REMBRANDTS.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/_R/REMBRANDTS.R b/src/_R/REMBRANDTS.R index 3f641c4..2e29904 100644 --- a/src/_R/REMBRANDTS.R +++ b/src/_R/REMBRANDTS.R @@ -1,4 +1,4 @@ -library(gplots) +suppressMessages(suppressWarnings(library (gplots))) ########### Identify the input arguments From 1ca473ec1fede5481f96e97c4f71819cf978247c Mon Sep 17 00:00:00 2001 From: abearab Date: Mon, 28 Aug 2023 22:11:03 -0700 Subject: [PATCH 6/7] update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 41c9cb8..6fae2ab 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ REMBRANDTS is a package for analysis of RNA-seq data across multiple samples in ### Requirements 1. Unix-compatible OS -2. [R](https://www.r-project.org/) version 3.2.3 or later +2. [R](https://www.r-project.org/) version 3.2.3 or later (tested on 4.3.1) 3. R [gplots](https://cran.r-project.org/web/packages/gplots/index.html) library 4. R [DEseq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) library (previously [DESeq](http://bioconductor.org/packages/release/bioc/html/DESeq.html)) From aefea9d97935cc2658df5a99a0cf68e2c229602a Mon Sep 17 00:00:00 2001 From: "Abolfazl (Abe)" Date: Fri, 15 Dec 2023 19:49:02 -0800 Subject: [PATCH 7/7] add doi badge --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 6fae2ab..4ae1c53 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ +[![DOI:10.1038/s41467-017-00867-z](https://zenodo.org/badge/DOI/DOI-10.1038/s41467-017-00867-z.svg)](https://doi.org/10.1038/s41467-017-00867-z) + # REMBRANDTS ### REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability