DOI: 10.18129/B9.bioc.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>

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biocViews DNASeq, PooledScreens, RNASeq, Software, VariantDetection
Version 1.12.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 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
Suggests testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
SystemRequirements Ensembl VEP, Samtools
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