DOI: 10.18129/B9.bioc.MMAPPR2    

This is the development version of MMAPPR2; for the stable release version, see MMAPPR2.

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Bioconductor version: Development (3.17)

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>

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


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

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

# The following initializes usage of Bioc devel


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


PDF   Reference Manual


biocViews DNASeq, PooledScreens, RNASeq, Software, VariantDetection
Version 1.13.0
In Bioconductor since BioC 3.10 (R-3.6) (3 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
Suggests testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
SystemRequirements Ensembl VEP, Samtools
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: