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Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Bioconductor version: Release (3.18)

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 (from within R, enter citation("MMAPPR2")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews DNASeq, PooledScreens, RNASeq, Software, VariantDetection
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.6.0)
Imports ensemblVEP(>= 1.20.0), gmapR, Rsamtools, VariantAnnotation, BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools, magrittr, methods, grDevices, graphics, stats, utils, stringr, data.table
System Requirements Ensembl VEP, Samtools
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/ https://github.com/kjohnsen/MMAPPR2
Bug Reports https://github.com/kjohnsen/MMAPPR2/issues
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Suggests testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
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Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64) MMAPPR2_1.16.0.tgz
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Source Repository git clone https://git.bioconductor.org/packages/MMAPPR2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MMAPPR2
Bioc Package Browser https://code.bioconductor.org/browse/MMAPPR2/
Package Short Url https://bioconductor.org/packages/MMAPPR2/
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