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DESCRIPTION
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DESCRIPTION
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Package: MMAPPR2
Title: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
Version: 0.99.22
Authors@R: c(
person("Kyle", "Johnsen", email="[email protected]", role=c("aut")),
person('Nathaniel', 'Jenkins', role=c('aut')),
person('Jonathon', 'Hill', email='[email protected]', 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