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# geneXtendeR
<img src="https://cloud.githubusercontent.com/assets/9893806/16898879/d14647c6-4bba-11e6-93d5-90bc802ac8e9.png">
##### R/Bioconductor package for optimized functional annotation of ChIP-seq data
[](https://travis-ci.org/Bohdan-Khomtchouk/geneXtendeR)
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`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: https://bioconductor.org/packages/geneXtendeR/. 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:
https://bioconductor.org/packages/devel/geneXtendeR/
https://bioconductor.org/packages/release/geneXtendeR/
https://bioconductor.org/packages/3.6/geneXtendeR/
### 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](https://github.com/hadley/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("https://bioconductor.org/biocLite.R")
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("https://bioconductor.org/biocLite.R")
biocLite() ## R version 3.0 or later
```
### Citation
If you are using `geneXtendeR` in your work, please cite the paper (http://dx.doi.org/10.1101/082347) accordingly.
