Package: epiSeeker
Type: Package
Title: epiSeeker: an R package for Annotation, Comparison and
        Visualization of multi-omics epigenetic data
Version: 1.1.0
Authors@R: c(
    person(given = "Guangchuang", family = "Yu",       email = "guangchuangyu@gmail.com",      role = c("aut", "cre", "fnd"), comment = c(ORCID = "0000-0002-6485-8781")),
    person(given = "Ming",        family = "Li",       email = "limiang929@gmail.com",         role = "ctb"),
    person(given = "Qianwen",     family = "Wang",     email = "treywea@gmail.com",            role = "ctb"),
    person(given = "Yun",         family = "Yan",      email = "youryanyun@gmail.com",         role = "ctb"),
    person(given = "Hervé",       family = "Pagès",    email = "hpages.on.github@gmail.com",   role = "ctb"),
    person(given = "Michael",     family = "Kluge",    email = "michael.kluge@bio.ifi.lmu.de", role = "ctb"),
    person(given = "Thomas",      family = "Schwarzl", email = "schwarzl@embl.de",             role = "ctb"),
    person(given = "Zhougeng",    family = "Xu",       email = "xuzhougeng@163.com",           role = "ctb"),
    person(given = "Chun-Hui",    family = "Gao",      email = "gaospecial@gmail.com",         role = "ctb")
    )
Description: This package implements functions to analyze multi-omics
        epigenetic data. Data of fragment type and base type are
        supported by epiSeeker. It provides functions to retrieve the
        nearest genes around the peak, annotate genomic region of the
        peak, statistical methods to estimate the significance of
        overlap among peak data sets, and motif analysis. It
        incorporates the GEO database for users to compare their own
        dataset with those deposited in the database. The comparison
        can be used to infer cooperative regulation and thus can be
        used to generate hypotheses. Several visualization functions
        are implemented to summarize the coverage of the peak
        experiment, average profile and heatmap of peaks binding to TSS
        regions, genomic annotation, distance to TSS, overlap of peaks
        or genes, and the single-base resolution epigenetic data by
        considering the strand, motif, and additional information.
Depends: R (>= 4.5.0)
Imports: AnnotationDbi, aplot, bsseq, BiocGenerics, Biostrings, boot,
        dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges,
        GenomicFeatures, ggplot2, graphics, grDevices, magrittr,
        methods, plotrix, parallel, RColorBrewer, rlang, RSQLite,
        rtracklayer, S4Vectors, scales, stats, SummarizedExperiment,
        tibble, tidyselect, tidyr, utils, yulab.utils (>= 0.2.0), grid
Suggests: ape, BSgenome, BSgenome.Hsapiens.UCSC.hg38, clusterProfiler,
        data.table, GEOmetadb, GEOquery, gggenes, ggimage, ggiraph,
        ggplotify, ggtree, gginnards, gridBase, gtools, ggupset,
        ggVennDiagram, JASPAR2024, knitr, org.Hs.eg.db, prettydoc,
        ReactomePA, rmarkdown, testthat, TFBSTools,
        TxDb.Hsapiens.UCSC.hg38.knownGene, universalmotif
URL: https://github.com/YuLab-SMU/epiSeeker
BugReports: https://github.com/YuLab-SMU/epiSeeker/issues
Encoding: UTF-8
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
biocViews: Annotation, ChIPSeq, Software, Visualization,
        MultipleComparison, Coverage, MotifAnnotation, GeneRegulation
RoxygenNote: 7.3.3
LazyData: false
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:06:06 UTC
RemoteUrl: https://github.com/bioc/epiSeeker
RemoteRef: HEAD
RemoteSha: 03bc0c589981d5ed5f1109d7517bca6e1f613bac
NeedsCompilation: no
Packaged: 2026-05-19 10:25:38 UTC; root
Author: Guangchuang Yu [aut, cre, fnd] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>),
  Ming Li [ctb],
  Qianwen Wang [ctb],
  Yun Yan [ctb],
  Hervé Pagès [ctb],
  Michael Kluge [ctb],
  Thomas Schwarzl [ctb],
  Zhougeng Xu [ctb],
  Chun-Hui Gao [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Built: R 4.6.0; ; 2026-05-19 10:33:58 UTC; windows
