boll3/rocker_transcriptomics repository overview

⁠Rocker Transcriptome Analysis

Here, we built a docker container specifically designed for transcriptomics data analysis. We utilize the rocker/verse container and extend them by several R packages from CRAN and Bioconductor to ensure a reproducible working environment.

⁠rocker/verse

The rocker project⁠ offers version-stable rocker images with rstudio server. The particular rocker/verse images⁠ are extended by tidyverse packages as well as tex and publishing-related packages.

Current rocker/verse version: 4.1.0⁠

⁠Additions:

In order to be able to run transcriptomics analysis, we extended the rocker/verse container by several R packages from CRAN and Bioconductor.

⁠Bioconductor packages

Plotting and visuals

• EnhancedVolcano
• karyoploteR
• enrichplot

Differential gene expression analysis

• DESeq2
• IHW
• sva
• RUVSeq

Functional characterization

• fgsea
• multiGSEA
• clusterProfiler
• EGSEA

Annotation

• org.Rn.eg.db
• org.Hs.eg.db
• org.Mm.eg.db
• org.Dr.eg.db
• biomaRt
• AnnotationHub
• metaboliteIDmapping
• BSgenome.Rnorvegicus.UCSC.rn6

⁠CRAN packages

• Rcpp
• BiocParallel
• hexbin
• apeglm
• ashr
• glmpca
• pheatmap
• eulerr
• PoiClaClu
• msigdbr
• gtools
• DT
• proj4
• WGCNA
• msigdbr
• bookdown
• gridExtra
• xtable
• ggnewscale
• ggupset
• ggridges