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Status](https://coveralls.io/repos/github/sjessa/chromswitch/badge.svg)](https://coveralls.io/github/sjessa/chromswitch)\n\n# `chromswitch`: An R/Bioconductor package for detecting chromatin state switches\n\n`chromswitch` implements a flexible method to detect chromatin state \nswitches between samples in two biological conditions in a specific genomic\nregion of interest given peaks or chromatin state calls from ChIP-seq data.\n\nNOTE: chromswitch is now deprecated: https://bioconductor.org/packages/3.17/bioc/html/chromswitch.html\n\n# Method\n\nThe `chromswitch` paper is now published _Bioinformatics_:\n\n\u003e 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)\n\nFor 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\u0026Signature=MOHlKYzBdR7bNc64a2G-k5eg2TofADoXEVwFUF94ymNUy0U1CuhnvuY1G2PatkwY7toY2svdhLdnivFQZajRfVrEZrMTVaaFV9qEowwIV3OJUmyUbBX2sFR9Hm17yvkFBwhJYjr-Hjek~Q3wXbGVZ7shO8kTJwgiSCaFFI0gbO3qz3PB80tq1NQllArBuZ01qTjxh1eKHUldljsjAOG2jDYHOVHMHQOZwyyiNkhhwvtE~RbdmpmV4y-AqkHiJB4sy~hIT3PyqD67LyEJMndVoNgCa76MaqUVjhH-l6I53f4kQCNtc7tfD2Q8vshU0whtXZUdNAvHIMPTxVNazsiEjA__\u0026Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q).\n\n\n# Installation\n\n~`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:~\n\nThe chromswitch BioConductor package is now deprecated.\n\n```r\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"chromswitch\")\n```\n\n\nFor 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:\n\n```\nbrowseVignettes(\"chromswitch\")\n```\n\n# Issues\n\nBug reports and issues are welcome, please [open an issue](https://github.com/sjessa/chromswitch/issues/new) in the GitHub\nrepository.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsjessa%2Fchromswitch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsjessa%2Fchromswitch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsjessa%2Fchromswitch/lists"}