kjohnsen/MMAPPR2: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

MMAPPR2 maps mutations resulting from pooled RNA-seq data from the F2 cross of forward genetic screens. Its predecessor is described in a paper published in Genome Research (Hill et al. 2013). MMAPPR2 accepts aligned BAM files as well as a reference genome as input, identifies loci of high sequence disparity between the control and mutant RNA sequences, predicts variant effects using Ensembl's Variant Effect Predictor, and outputs a ranked list of candidate mutations.

Getting started

Package details

Bioconductor views DNASeq PooledScreens RNASeq VariantDetection
Maintainer
LicenseGPL-3
Version0.99.2
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/ https://github.com/kjohnsen/MMAPPR2
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("kjohnsen/MMAPPR2")
kjohnsen/MMAPPR2 documentation built on Oct. 24, 2018, 10:14 p.m.