boll3/rocker_multiomics repository overview

⁠Rocker Multi-Omics Analysis

Here, we built a docker container specifically designed for multi-omics 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: 4.1.2⁠

⁠Additions:

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

⁠Bioconductor packages

Multi-omics analysis

• MOFA2
• mixOmics

Plotting and visuals

• EnhancedVolcano
• enrichplot

Tools for single-omics analysis and data preparation

• DESeq2
• limma
• DEP

Functional characterization

• fgsea
• multiGSEA
• clusterProfiler
• EGSEA

Annotation

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

⁠CRAN packages

• Rcpp
• BiocParallel
• hexbin
• eulerr
• pheatmap
• msigdbr
• gtools
• DT
• proj4
• bookdown
• gridExtra
• xtable
• ggnewscale
• ggupset
• ggridges
• reticulate