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<div align="center"> # geneXtendeR <img src=""> ##### R/Bioconductor package for optimized functional annotation of ChIP-seq data [![Travis-CI Build Status](]( [![AUR](]() [![Bioconductor Time](]( "Bioconductor status") [![Bioconductor Downloads](]( "Percentile downloads") [![Bioconductor Commits](]( "svn commits") [![Support posts](]( "Bioconductor support posts") </div> `geneXtendeR` optimizes the functional annotation of ChIP-seq peaks using fast iterative peak-coordinate/GTF alignment algorithms. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can be a noisy process. As such, the goal of `geneXtendeR` is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR. ### Landing page `geneXtendeR` can be found at: This URL will redirect to the release landing page of the package and is the URL that should be used (in publications, etc.) to refer to `geneXtendeR`. You can also refer specifically to the development, release, or specific numbered version of Bioconductor: ### Vignette Please read the `geneXtendeR` documentation (`geneXtendeR.pdf` found in the `/vignettes` directory), which includes software workflows and comprehensive analyses to get you started. ### Github installation instructions You can install the current GitHub version using the [devtools]( package: ```R if (!require("devtools")) install.packages("devtools") devtools::install_github("Bohdan-Khomtchouk/geneXtendeR") ``` And then load the package: ```R library(geneXtendeR) ``` ### Bioconductor installation instructions ```R ## try http:// if https:// URLs are not supported source("") biocLite("geneXtendeR") ``` After installation, you should always update to the latest available version of `geneXtendeR` by typing `biocLite()`: ```R ## try http:// if https:// URLs are not supported source("") biocLite() ## R version 3.0 or later ``` ### Citation If you are using `geneXtendeR` in your work, please cite the paper ( accordingly.