[](https://travis-ci.org/sjessa/chromswitch) [](https://coveralls.io/github/sjessa/chromswitch) # `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. # 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](https://doi.org/10.1093/bioinformatics/bty075) For details on the method, see the [Supplementary Methods](https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/bioinformatics/PAP/10.1093_bioinformatics_bty075/2/bty075_supp.pdf?Expires=1523314027&Signature=MOHlKYzBdR7bNc64a2G-k5eg2TofADoXEVwFUF94ymNUy0U1CuhnvuY1G2PatkwY7toY2svdhLdnivFQZajRfVrEZrMTVaaFV9qEowwIV3OJUmyUbBX2sFR9Hm17yvkFBwhJYjr-Hjek~Q3wXbGVZ7shO8kTJwgiSCaFFI0gbO3qz3PB80tq1NQllArBuZ01qTjxh1eKHUldljsjAOG2jDYHOVHMHQOZwyyiNkhhwvtE~RbdmpmV4y-AqkHiJB4sy~hIT3PyqD67LyEJMndVoNgCa76MaqUVjhH-l6I53f4kQCNtc7tfD2Q8vshU0whtXZUdNAvHIMPTxVNazsiEjA__&Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q). # Installation `chromswitch` is available from Bioconductor at [bioconductor.org/packages/chromswitch](https://bioconductor.org/packages/release/bioc/html/chromswitch.html). To install the package from the R console: ```r install.packages("BiocManager") BiocManager::install("chromswitch") ``` For an introduction to the package, check out the [vignette](https://bioconductor.org/packages/release/bioc/vignettes/chromswitch/inst/doc/chromswitch_intro.html), or open it from the R console: ``` browseVignettes("chromswitch") ``` # Issues Bug reports and issues are welcome, please [open an issue](https://github.com/sjessa/chromswitch/issues/new) in the GitHub repository.