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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("AllelicImbalance","pappewaio")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