lbwang/rocker-transcriptome repository overview

⁠Docker image of R, RStudio, and genomic tools

This repo builds various R Docker images for genomic analysis:

• lbwang/rocker-genome⁠
• lbwang/rocker-transcriptome⁠

⁠lbwang/rocker-genome

The docker image builds on top of the Docker image rocker/tidyverse⁠ and includes useful R packages for genomic data:

• plyr-like grammars:

  • plyranges

• Visualization:

  • pheatmap
  • ComplexHeatmap
  • gtrellis
  • ggrepel
  • ggbeeswarm
  • viridis
  • colorspace

• Genome annotation:

  • ensembldb

• Multiple testing correction:

  • fdrtool
  • qvalue

• File I/O:

  • vroom
  • zstd (Zstandard; not a R package)

The full list of installed R packages can be found at installed_packages.rocker-genome.tsv⁠.

⁠Derived docker images

⁠lbwang/rocker-transcriptome

The docker images includes R packages for transcriptome analysis:

• tximport
• DESeq2
• apeglm
• vsn
• clusterExperiment
• ConsensusClusterPlus

The full list of installed R packages can be found at installed_packages.rocker-transcriptome.tsv⁠.

⁠Utility

The command to update the list of installed R packages:

bash gen_all_pkg_lists.sh