chromswitch: An R/Bioconductor package for detecting chromatin state switches

chromswitch implements a flexible method to detect chromatin state switches between samples in two biological conditions in a specific genomic region of interest given peaks or chromatin state calls from ChIP-seq data.

NOTE: chromswitch is now deprecated: https://bioconductor.org/packages/3.17/bioc/html/chromswitch.html

Method

The chromswitch paper is now published Bioinformatics:

Selin Jessa, Claudia L Kleinman (2018). chromswitch: a flexible method to detect chromatin state switches, Bioinformatics, https://doi.org/10.1093/bioinformatics/bty075

For details on the method, see the Supplementary Methods.

Installation

chromswitch is available from Bioconductor at bioconductor.org/packages/chromswitch. To install the package from the R console:

The chromswitch BioConductor package is now deprecated.

install.packages("BiocManager")
BiocManager::install("chromswitch")

For an introduction to the package, check out the vignette, or open it from the R console:

browseVignettes("chromswitch")

Issues

Bug reports and issues are welcome, please open an issue in the GitHub repository.