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 byu.edu>

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

Installation

To install this package, start R (version "4.2") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MMAPPR2")

An Introduction to MMAPPR2	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNASeq, PooledScreens, RNASeq, Software, VariantDetection
Version	1.12.0
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

Suggests	testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle, MMAPPR2data
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MMAPPR2_1.12.0.tar.gz
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
Bioc Package Browser	https://code.bioconductor.org/browse/MMAPPR2/
Package Short Url	https://bioconductor.org/packages/MMAPPR2/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive