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