puweilin / fastde

FastDE

This is an R package for performing differential gene expression analysis. It is designed as a drop-in replacement for the Seurat FindAllMarkers function.

The goal of the library is to improve computational performance and large scale data handling.

Currently, Seurat supports 9 algorithms. FastDE supports student's t-test and Wilcox Rank Sum test.

Installation

From Bioconductor

BiocManager::install("fastde")

From source.

devtools::install_github("tcpan\fastde.git")

BiocManager::install(c("argparser", "SCnorm", "sva", "limma", "SingleCellExperiment", "edgeR"), lib=.libPaths()[1])

BiocManager::install(c("future", "future.apply", "stringi", "reshape2", "magrittr", "tidyr", "fastcluster", "diceR"), lib=.libPaths()[1])

BiocManager::install(c("proftools", "profvis", "tictoc"), lib=.libPaths()[1])