xcore

xcore is an R package for transcription factor activity modeling based on known molecular signatures and user’s gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments.

We refer interested users to our publication in BMC Bioinformatics.

Installation

xcore and xcoredata can be installed from Bioconductor:

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

BiocManager::install("xcore")
BiocManager::install("xcoredata")

Usage

A vignette showing xcore basic usage is available here.

Parallel computing

xcore can take advantage of parallelization to speed up calculations, especially for model training and estimates testing. To use parallel computing in R one have to first register parallel backend. While there are many parallel backends to choose from, internally xcore uses foreach to implement parallel computing. Having this in mind we should use a backend supported by foreach.

In the vignette we are using doParallel backend, together with BiocParallel package providing unified interface across different OS. Those packages can be installed with:

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

BiocManager::install("BiocParallel")
install.packages("doParallel")