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README.md

README.md

Status: Travis CI Build Status

Bioc-release

Bioc-devel

The Bioc-release and Bioc-devel builds are updated every day at 10:30AM Seattle time.

The latest bioconductor releases and the bioconductor development branch can be found either on github or at the home of bioconductor,

AllelicImbalance

A Bioconductor package for allelic imbalance analysis on RNA sequencing data. The aim is to support infrastructure for storage of summarized allele counts and functions to quickly retrieve important figures for AI analyses. The package also provides SNP or region specific visualization and interaction with other common bioconductor functionality.

See the "DESCRIPTION" file for additional requirements.

Documentation

The vignette provides an introduction to the allelic imbalance concept and show examples of how the AllelicImbalance package can be used to find AI-events and measure the global or local mapping bias from the alignment of RNA-seq reads to a reference genome.

Installation

Installation of the devel version of this package from Github requires the devtools package.

install.packages("devtools")
library(devtools)
install_github("pappewaio/AllelicImbalance")

Alternatively, you can easily install the release version of AllelicImbalance from Bioconductor.

source("http://bioconductor.org/biocLite.R")
biocLite("AllelicImbalance")

Citation

Jesper R. Gådin, Ferdinand M. van’t Hooft, Per Eriksson and Lasse Folkersen. (2015). AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing. BMC Bioinformatics. link

Bug Reports / Issues

The official development site for AllelicImbalance is at https://github.com/pappewaio/AllelicImbalance. For bug-reports / issues / comments regarding the development branch you may preferably submit there, and for the release version it might be more appropriate to submit at the bioconductor support-site which can be found HERE