DOI: 10.18129/B9.bioc.chromswitch  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see chromswitch.

An R package to detect chromatin state switches from epigenomic data

Bioconductor version: 3.17

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.

Author: Selin Jessa [aut, cre], Claudia L. Kleinman [aut]

Maintainer: Selin Jessa <selinjessa at>

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HTML R Script An introduction to `chromswitch` for detecting chromatin state switches
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biocViews Clustering, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneExpression, HistoneModification, ImmunoOncology, MultipleComparison, Software, Transcription
Version 1.22.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), GenomicRanges(>= 1.26.4)
Imports cluster (>= 2.0.6), Biobase(>= 2.36.2), BiocParallel(>= 1.8.2), dplyr (>= 0.5.0), gplots (>= 3.0.1), graphics, grDevices, IRanges(>= 2.4.8), lazyeval (>= 0.2.0), matrixStats (>= 0.52), magrittr (>= 1.5), methods, NMF (>= 0.20.6), rtracklayer(>= 1.36.4), S4Vectors(>= 0.23.19), stats, tidyr (>= 0.6.3)
Suggests BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb(>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat
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