risserlin/multiome_analysis repository overview

Base RStudio docker image with cell cell interaction tools installed.

based on bioconductor docker Release 3_19 - R4.4.1

includes packages - RColorBrewera, ggplot2, devtools, rmarkdown, htts, knitr, xaringan, bookdown, gprofiler2, seqinr, complexheatmap, biomaRt, geometadb, limma, edgeR, biogenerics, kableExtra, GSEABase, GSVA, BiocStyle, BiocParallel, RCy3, GSA, seurat, fgsea, SummarizedExperiment, pheatmap, RTCGAToolbox, GenomicDataCommons, recount, DESeq2

installed GSEA 4.3.2 jar ( so that GSEA can we run from the command line from within the docker

installed JAVA to be able to run GSEA

installed python 3 and umap-learn

For Cell chat install - BiocNeighbors and install from github jinworks/cellchat

Running this image:

docker run -v "$(pwd)":/home/rstudio/projects -e PASSWORD=password -p 8787:8787 --add-host="localhost:###.###.###.###" risserlin/multiome_analysis

Added packages specific to multiome data analysis SeuratObject, signac, AnnotationDbi