Package: QuasR
Type: Package
Title: Quantify and Annotate Short Reads in R
Version: 1.30.0
Date: 2020-10-09
Author: Anita Lerch, Charlotte Soneson, Dimos Gaiditzis and Michael Stadler
Maintainer: Michael Stadler <michael.stadler@fmi.ch>
Depends: R (>= 4.0), parallel, GenomicRanges, Rbowtie
Imports: methods, grDevices, graphics, utils, BiocGenerics,
	S4Vectors, IRanges, BiocManager, Biobase,
    Biostrings, BSgenome, Rsamtools,
    GenomicFeatures, ShortRead,
    GenomicAlignments, BiocParallel, GenomeInfoDb,
    rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi
Suggests: 
    Gviz,
    BiocStyle,
    knitr,
    rmarkdown,
    covr,
    testthat
LinkingTo: Rhtslib
SystemRequirements: GNU make
Description: This package provides a framework for the quantification
    and analysis of Short Reads. It covers a complete workflow
    starting from raw sequence reads, over creation of alignments
    and quality control plots, to the quantification of genomic
    regions of interest.
License: GPL-2
biocViews: Genetics, Preprocessing, Sequencing, ChIPSeq, RNASeq,
    MethylSeq, Coverage, Alignment, QualityControl, ImmunoOncology
Archs: x64
VignetteBuilder: knitr