Package: qsea
Type: Package
Title: IP-seq data analysis and vizualization
Version: 1.35.1
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: 2025-10-07 23:31:48 UTC; biocbuild
NeedsCompilation: yes
git_url: https://git.bioconductor.org/packages/qsea
git_branch: devel
git_last_commit: 7800f67
git_last_commit_date: 2025-07-23
Repository: Bioconductor 3.22
Date/Publication: 2025-10-07
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>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-29 21:03:33 UTC; windows
Archs: x64
