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MMAPPR2

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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 (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MMAPPR2")

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

Documentation

Reference Manual PDF

Details

biocViews DNASeq, PooledScreens, RNASeq, Software, VariantDetection
Version 1.17.1
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
See More
Suggests testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64) MMAPPR2_1.17.1.tgz
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/
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