jsschrepping/r_docker repository overview

R studio docker container for scRNA-seq analyses build on bioconductor_docker:RELEASE_3_16 and R v4.2.2.

Installed R packages include:

• DESeq2

• tximport

• limma

• edgeR

• complexheatmap

• EnhancedVolcano

• clusterProfiler

• gage

• monocle & monocle3

• slingshot

• SingleCellExperiment

• Seurat v4.2.1

• SeuratDisc

• SingleR

• Rcistarget

• harmony

• symphony

• SoupX

• AUcell

• Ucell

• DittoSeq

• DiffBind

• ChipSeeker

• Signac

• ArchR

• Gviz

• ChromVar

• Human Annotation databases (org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, EnsDb.Hsapiens.v86)

and many more...

In addition, following python packages are installed to be used via reticulate:

• MACS3
• Cytosig
• scanpy
• scvelo
• cellrank
• scrublet

(CellphoneDB had to be removed due to incompatibilities with python versions.)

Installed versions of packages are documented in install_log.txt For instructions on how to launch RStudio in docker please read: https://ropenscilabs.github.io/r-docker-tutorial/02-Launching-Docker.html⁠.