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")