# xcore xcore is an R package for transcription factor activity modeling based on known molecular signatures and user's gene expression data. Accompanying [xcoredata](https://github.com/mcjmigdal/xcoredata/) package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. We refer interested users to our [bioRxiv preprint](https://www.biorxiv.org/content/10.1101/2022.02.23.481130v1). ## Installation xcore and xcoredata can be installed from Bioconductor: ``` r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("xcore") BiocManager::install("xcoredata") ``` ## Usage A vignette showing xcore basic usage is available [here](https://bkaczkowski.github.io/xcore/articles/xcore_vignette.html). ## 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`](https://cran.r-project.org/web/packages/foreach) to implement parallel computing. Having this in mind we should use a backend supported by `foreach`. In the vignette we are using [`doParallel`](https://cran.r-project.org/package=doParallel) backend, together with [`BiocParallel`](https://bioconductor.org/packages/release/bioc/html/BiocParallel.html) package providing unified interface across different OS. Those packages can be installed with: ``` r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BiocParallel") install.packages("doParallel") ```