Package: MMAPPR2
Title: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
Version: 1.0.0
Authors@R: c(
    person("Kyle", "Johnsen", email="kjohnsen@byu.edu", role=c("aut")),
    person('Nathaniel', 'Jenkins', role=c('aut')),
    person('Jonathon', 'Hill', email='jhill@byu.edu', role=c('cre')))
Description: 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.
Depends: R (>= 3.6.0)
License: GPL-3
Encoding: UTF-8
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Suggests: testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle,
        MMAPPR2data
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
SystemRequirements: Ensembl VEP, Samtools
biocViews: RNASeq, PooledScreens, DNASeq, VariantDetection
URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613585/,
        https://github.com/kjohnsen/MMAPPR2
BugReports: https://github.com/kjohnsen/MMAPPR2/issues
OS_type: unix
git_url: https://git.bioconductor.org/packages/MMAPPR2
git_branch: RELEASE_3_10
git_last_commit: 50c8222
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: no
Packaged: 2019-10-30 03:43:59 UTC; biocbuild
Author: Kyle Johnsen [aut],
  Nathaniel Jenkins [aut],
  Jonathon Hill [cre]
Maintainer: Jonathon Hill <jhill@byu.edu>
