ChromstaR is a versatile ChIP-seq analysis suite with the following features:
ChromstaR is a powerful tool for any type of ChIP-seq analysis. For instance, you can use it to find bivalent promoters, poised enhancers etc. between two or more experimental conditions. It implements high-quality peak calling for broad and narrow marks and enables combinatorial and differential chromatin state analysis. It provides ready-to-use functions for any type of enrichment analysis and results can easily be assessed in a genome browser. The method is described here and a tutorial is available here.
Please visit also the website at https://chromstar.org/.
To install the current stable version from Bioconductor, please visit http://bioconductor.org/packages/release/chromstaR/ and follow the provided instructions.
To install the development version from Github, follow the steps given below. The installation has only been tested on Ubuntu so far, if you need to install on Windows or Mac additional steps might be necessary (e.g. installation of Rtools from https://cran.r-project.org/bin/windows/Rtools/)
install.packages("devtools") if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install(c("GenomicRanges","GenomicAlignments","bamsignals")) library(devtools) install_github("ataudt/chromstaRData") install_github("ataudt/chromstaR") #### Or alternatively if the above line doesn't work: install_git("git://github.com/ataudt/chromstaRData.git", branch = "master") install_git("git://github.com/ataudt/chromstaR.git", branch = "master")
Please refer to the vignette for tutorials on all chromstaR features.
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