MMAPPR2

DOI: 10.18129/B9.bioc.MMAPPR2  

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>

Installation

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

PDF		Reference Manual

Details

biocViews	DNASeq, PooledScreens, RNASeq, Software, VariantDetection
Version	1.16.0
In Bioconductor since	BioC 3.10 (R-3.6) (4 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
LinkingTo
Suggests	testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
SystemRequirements	Ensembl VEP, Samtools
Enhances
URL	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/ https://github.com/kjohnsen/MMAPPR2
BugReports	https://github.com/kjohnsen/MMAPPR2/issues
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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 https://git.bioconductor.org/packages/MMAPPR2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MMAPPR2
Package Short Url	https://bioconductor.org/packages/MMAPPR2/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive