/r_docker

Docker container for genomics analyses in R.

Primary LanguageRMIT LicenseMIT

R studio docker container for scRNA-seq analyses build on bioconductor_docker:RELEASE_3_17 and R v4.3.0.

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

  • CytoExploreR

  • CytoML

  • FlowWorkspace

  • ggcyto

  • openCyto

  • cydar

  • 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.