README.md

DESeq2

Workflow used for differential gene expression analysis

DESeq2 docs

• https://bioconductor.org/packages/release/bioc/html/DESeq2.html

Importing kallisto output with tximport

• https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto

Run pure script (to test)

Install R dependencies for deseq2

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")
library("DESeq2")

BiocManager::install("tximport")
library("tximport")

BiocManager::install("rhdf5")
library("rhdf5")

test

RScript deseq2.R "../../runs/kallisto/kallisto_results" "../../runs/merged_isa_metadata/out/merged_isa.tsv" "Source.Name" "Factor..Photosynthesis.mode."

Multi-package containers

• R and combinations of library dependencies are available as multi-package containers from BioContainers
• Searched for repo:BioContainers/multi-package-containers deseq2 tximport rhdf5
• and found quay.io/biocontainers/mulled-v2-05fd88b9ac812a9149da2f2d881d62f01cc49835:a10f0e3a7a70fc45494f8781d33901086d2214d0-0 🎉