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# 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 [bioRxiv preprint]( ## 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]( ## 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: ``` r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BiocParallel") install.packages("doParallel") ```