Package: qsea
Type: Package
Title: IP-seq data analysis and vizualization
Version: 1.39.0
Date: 2025-07-22
Authors@R: c(
        person("Matthias", "Lienhard", role=c("aut", "cre"), email="lienhard@molgen.mpg.de", comment = c(ORCID = "0000-0002-2549-3142")),
        person("Lukas", "Chavez", role="aut", comment = c(ORCID = "0000-0002-8718-8848")),
        person("Ralf", "Herwig", role="aut", comment = c(ORCID = "0000-0002-9335-1760")))
Description: qsea (quantitative sequencing enrichment analysis) was
        developed as the successor of the MEDIPS package for analyzing
        data derived from methylated DNA immunoprecipitation (MeDIP)
        experiments followed by sequencing (MeDIP-seq). However, qsea
        provides several functionalities for the analysis of other
        kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq,
        CMS-seq and others) including calculation of differential
        enrichment between groups of samples.
License: GPL-2
biocViews: Sequencing, DNAMethylation, CpGIsland, ChIPSeq,
        Preprocessing, Normalization, QualityControl, Visualization,
        CopyNumberVariation, ChipOnChip, DifferentialMethylation
Depends: R (>= 4.3)
Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy,
        rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges,
        limma, Seqinfo, BiocGenerics, grDevices, zoo, BiocParallel,
        S4Vectors
VignetteBuilder: knitr
Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle,
        knitr, rmarkdown, BiocManager, MASS
ByteCompile: no
Packaged: 2026-07-04 03:48:16 UTC; root
NeedsCompilation: yes
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:43:45 UTC
RemoteUrl: https://github.com/bioc/qsea
RemoteRef: HEAD
RemoteSha: 167cec0c91702cacbfb01090bf60a13354e511e2
Author: Matthias Lienhard [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2549-3142>),
  Lukas Chavez [aut] (ORCID: <https://orcid.org/0000-0002-8718-8848>),
  Ralf Herwig [aut] (ORCID: <https://orcid.org/0000-0002-9335-1760>)
Maintainer: Matthias Lienhard <lienhard@molgen.mpg.de>