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MMAPPR2
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MMAPPR2.
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
Bioconductor version: 3.16
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.
Author: Kyle Johnsen [aut], Nathaniel Jenkins [aut], Jonathon Hill [cre]
Maintainer: Jonathon Hill <jhill at byu.edu>
citation("MMAPPR2")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MMAPPR2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MMAPPR2")
Details
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Follow Installation instructions to use this package in your R session.