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README.md 100644 2 kb
README.md
chromstaR ========= This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses. For a quick introduction on how to use the package, [read this](https://github.com/ataudt/chromstaR/blob/master/vignettes/chromstaR.pdf). The method is described [here](http://biorxiv.org/content/early/2016/02/04/038612). Installation ------------ ### Stable release version from Bioconductor (not available yet) To install the *current stable* version from Bioconductor, please visit http://bioconductor.org/packages/chromstaR/ and follow the provided instructions. ### Development version from Github 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/) 1. Install a recent version of R (>=3.2.0) from https://www.r-project.org/ 2. Optional: For ease of use, install Rstudio from https://www.rstudio.com/ 3. Open R and install all dependencies. Please ensure that you have writing permissions to install packages. Execute the following lines one by one: install.packages("devtools") source("http://bioconductor.org/biocLite.R") biocLite(c("GenomicRanges","GenomicAlignments")) 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") How to use chromstaR -------------------- Please refer to the vignette at https://github.com/ataudt/chromstaR/blob/master/vignettes/chromstaR.pdf for tutorials on all chromstaR features. Report Errors ------------- If you encounter errors of any kind, please file an [issue here](https://github.com/ataudt/chromstaR/issues/new). I will try to react within one day.