This repo builds various R Docker images for genomic analysis:
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
.
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
.
The command to update the list of installed R packages:
bash gen_all_pkg_lists.sh