R packages

List of R packages used

CRAN

• data.table: https://cran.r-project.org/package=data.table

• dplyr: https://cran.r-project.org/package=dplyr

• reshape2: https://cran.r-project.org/package=reshape2

• ggplot2: https://cran.r-project.org/package=ggplot2

• ggrepel: https://cran.r-project.org/package=ggrepel

• ggbeeswarm: https://cran.r-project.org/package=ggbeeswarm

Bioconductor

• GenomicFeatures: https://bioconductor.org/packages/GenomicFeatures/

• tximport: https://bioconductor.org/packages/tximport/

• DESeq2: https://bioconductor.org/packages/DESeq2/

• apeglm: https://bioconductor.org/packages/apeglm/

• EnhancedVolcano: https://bioconductor.org/packages/EnhancedVolcano/

• DRIMSeq: https://bioconductor.org/packages/DRIMSeq/

• DEXSeq: https://bioconductor.org/packages/DEXSeq/

• stageR: https://www.bioconductor.org/packages/stageR/

• edgeR: https://www.bioconductor.org/packages/edgeR/

GitHub

• wasabi: https://github.com/COMBINE-lab/wasabi

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

BiocManager::install("devtools")    # only if devtools not yet installed
BiocManager::install("COMBINE-lab/wasabi")

• sleuth: https://github.com/pachterlab/sleuth

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

BiocManager::install("devtools")    # only if devtools not yet installed
BiocManager::install("pachterlab/sleuth")