ExprX - an R package to streamline interspecies differential expression analysis

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ExprX is an R package to streamline interspecies differential expression analysis. Taking TPM or FPKM/RPKM files for samples from different species as input, it provides functions to handle all the necessary steps, including data loading, ortholog matching, normalization, differential analysis and visualization.

How to install ExprX

ExprX can be installed using the install_git function from devtools package. However, it depends on several other R packages, which should be installed first.

To install ExprX and its dependencies:

install.packages("BiocManager")

BiocManager::install(c("biomaRt", "edgeR", "RankProd"))

install.packages("devtools")

devtools::install_git("https://github.com/mingansun/ExprX")

To load the ExprX package:

library(ExprX)

How to use ExprX

Please refer to the Vignette about how to use ExprX to perform interspecies differential expression analysis. The PDF version of Vignette can be downloaded from:

https://github.com/mingansun/ExprX/blob/master/inst/doc/ExprX-vignette.pdf

Citation:

Sun MA, Wolf G, Wang Y, Senft AD, Ralls S, Jin J, Dunn-Fletcher CE, Muglia LJ, Macfarlan TS. 2021. Endogenous retroviruses drive lineage-specific regulatory evolution across primate and rodent placentae. Mol Biol Evol 38: 4992–5004.