paper_deconvBenchmark/Libraries.R at master · LiuzLab/paper_deconvBenchmark · GitHub

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# Plot relevant libraries (cran)
library(ggplot2)
library(gridExtra)
library(cowplot)
library(pheatmap)
library(RColorBrewer)
library(LSD)


# RNA-seq analysis relevant libraries (Bioconductor)
library(edgeR)
library(DESeq2)
library(fgsea)
library(genefilter)
library(biomaRt)
library(limma)
library(scater)


# other libraries (cran)
library(reshape)
library(reshape2)
library(plyr)
library(scales)
library(xbioc)

# Deconvolution relevant libraries (Bioconductor unless marked differently)
library(CAMTHC)
library(DeconRNASeq)
library(MuSiC) # Github: https://github.com/xuranw/MuSiC
library(linseed) # Github: https://github.com/ctlab/LinSeed
library(DSA) # Github: https://github.com/zhandong/DSA
library(EPIC) # Github: https://github.com/GfellerLab/EPIC