diff --git a/README.md b/README.md index 5d26b9d..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 @@ -7,9 +9,9 @@ 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 [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 diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..1f7511c --- /dev/null +++ b/environment.yml @@ -0,0 +1,9 @@ +name: stbl +channels: + - conda-forge + - bioconda +dependencies: + - bioconductor-deseq2 + - r-gplots + - r-tibble + - ipykernel 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) 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