Package: QuasR
Type: Package
Title: Quantify and Annotate Short Reads in R
Version: 1.53.0
Date: 2025-06-23
Authors@R: c(person("Anita", "Lerch", role = c("aut")),
             person("Adam Alexander Thil", "SMITH", role = c("aut"), 
                    email = "alex.smith@fmi.ch", 
                    comment = c(ORCID = "0000-0003-4593-3042")),
             person("Charlotte", "Soneson", role = c("aut"), 
                    email = "charlottesoneson@gmail.com", 
                    comment = c(ORCID = "0000-0003-3833-2169")),
             person("Dimos", "Gaidatzis", role = c("aut")),
             person("Michael", "Stadler", role = c("aut", "cre"), 
                    email = "michael.stadler@fmi.ch", 
                    comment = c(ORCID = "0000-0002-2269-4934")))
Depends: R (>= 4.4), parallel, GenomicRanges, Rbowtie
Imports: methods, grDevices, graphics, utils, stats, tools,
        BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings,
        BSgenome, Rsamtools (>= 2.13.1), GenomicFeatures, txdbmaker,
        ShortRead, BiocParallel, Seqinfo, rtracklayer, GenomicFiles,
        AnnotationDbi
Suggests: Gviz, BiocStyle, GenomeInfoDbData, GenomicAlignments,
        Rhisat2, knitr, rmarkdown, covr, testthat
LinkingTo: Rhtslib (>= 1.99.1)
Encoding: UTF-8
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. Read alignments are either generated
        through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments)
        or Rhisat2 (data from RNA-seq experiments that require spliced
        alignments), or can be provided in the form of bam files.
URL: https://bioconductor.org/packages/QuasR
License: GPL-2
biocViews: Genetics, Preprocessing, Sequencing, ChIPSeq, RNASeq,
        MethylSeq, Coverage, Alignment, QualityControl, ImmunoOncology
Archs: x64
VignetteBuilder: knitr
RoxygenNote: 7.3.2
BugReports: https://github.com/fmicompbio/QuasR/issues
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:37:12 UTC
RemoteUrl: https://github.com/bioc/QuasR
RemoteRef: HEAD
RemoteSha: ead61df17f1aa244983cf783cd0c4263756d225e
NeedsCompilation: yes
Packaged: 2026-05-31 06:13:11 UTC; root
Author: Anita Lerch [aut],
  Adam Alexander Thil SMITH [aut] (ORCID:
    <https://orcid.org/0000-0003-4593-3042>),
  Charlotte Soneson [aut] (ORCID:
    <https://orcid.org/0000-0003-3833-2169>),
  Dimos Gaidatzis [aut],
  Michael Stadler [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2269-4934>)
Maintainer: Michael Stadler <michael.stadler@fmi.ch>