Package: EpiCompare
Type: Package
Title: Comparison, Benchmarking & QC of Epigenetic Datasets
Version: 1.0.0
Authors@R: 
    c(person(given = "Sera",
             family = "Choi",
             role = c("aut", "cre"),
             email = "serachoi1230@gmail.com",
             comment = c(ORCID = "0000-0002-5077-1984")),
      person(given = "Brian",
             family = "Schilder",
             role = c("aut"),
             email = "brian_schilder@alumni.brown.edu",
             comment = c(ORCID = "0000-0001-5949-2191")),
      person(given = "Alan",
             family = "Murphy",
             role = c("aut"),
             email = "alanmurph94@hotmail.com",
             comment = c(ORCID = "0000-0002-2487-8753")),
      person(given = "Nathan",
             family = "Skene",
             role = c("aut"),
             email = "nathan.skene@gmail.com",
             comment = c(ORCID = "0000-0002-6807-3180")))
Description: EpiCompare is used to compare and analyse epigenetic datasets 
  for quality control and benchmarking purposes. 
  The package outputs an HTML report consisting of three sections: 
  (1. General metrics) Metrics on peaks (percentage of blacklisted and 
  non-standard peaks, and peak widths) and fragments (duplication rate) 
  of samples, 
  (2. Peak overlap) Percentage and statistical significance of 
  overlapping and non-overlapping peaks. Also includes upset plot and 
  (3. Functional annotation) functional annotation 
  (ChromHMM, ChIPseeker and enrichment analysis) of peaks. 
  Also includes peak enrichment around TSS.
URL: https://github.com/neurogenomics/EpiCompare
BugReports: https://github.com/neurogenomics/EpiCompare/issues
License: GPL-3
Depends: R (>= 4.1.0)
LazyData: FALSE
biocViews: Epigenetics, Genetics, QualityControl, ChIPSeq,
        MultipleComparison, FunctionalGenomics, ATACSeq, DNaseSeq
Imports: GenomicRanges, genomation, IRanges, reshape2, ggplot2,
        ChIPseeker, BRGenomics, clusterProfiler, plotly, stringr,
        dplyr, tidyr, UpSetR, rmarkdown, rtracklayer, AnnotationHub,
        utils, stats, methods, org.Hs.eg.db, S4Vectors, magrittr,
        plyranges
Suggests: testthat (>= 3.0.0), badger, knitr, htmlwidgets, BiocStyle,
        data.table, BiocParallel, BiocFileCache,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Hsapiens.UCSC.hg38.knownGene
VignetteBuilder: knitr
RoxygenNote: 7.1.2.9000
Encoding: UTF-8
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/EpiCompare
git_branch: RELEASE_3_15
git_last_commit: fba3043
git_last_commit_date: 2022-04-27
Date/Publication: 2022-04-27
NeedsCompilation: no
Packaged: 2022-04-27 23:47:25 UTC; biocbuild
Author: Sera Choi [aut, cre] (<https://orcid.org/0000-0002-5077-1984>),
  Brian Schilder [aut] (<https://orcid.org/0000-0001-5949-2191>),
  Alan Murphy [aut] (<https://orcid.org/0000-0002-2487-8753>),
  Nathan Skene [aut] (<https://orcid.org/0000-0002-6807-3180>)
Maintainer: Sera Choi <serachoi1230@gmail.com>
Built: R 4.2.0; ; 2022-04-28 10:44:05 UTC; windows
