Package: extraChIPs
Version: 1.12.0
Title: Additional functions for working with ChIP-Seq data
Authors@R: person("Stevie", "Pederson", 
  email = "stephen.pederson.au@gmail.com", 
  role = c("aut", "cre"),
  comment = c(ORCID = "0000-0001-8197-3303")
  )
Description: This package builds on existing tools and adds some simple but
   extremely useful capabilities for working wth ChIP-Seq data. The focus is 
   on detecting differential binding windows/regions. 
   One set of functions focusses on set-operations retaining mcols for GRanges
   objects, whilst another group of functions are to aid visualisation of 
   results.
   Coercion to tibble objects is also implemented.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/smped/extraChIPs
BugReports: https://github.com/smped/extraChIPs/issues
Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0),
        ggside (>= 0.3.1), SummarizedExperiment, tibble
Imports: csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb,
        glue, ggrepel, InteractionSet, IRanges, matrixStats, methods,
        patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer,
        S4Vectors, scales, stats, stringr, tidyr, tidyselect, vctrs
Suggests: apeglm, BiocStyle, ComplexUpset, covr, DESeq2,
        EnrichedHeatmap, GenomicAlignments, GenomicInteractions, Gviz,
        ggforce, harmonicmeanp, here, knitr, limma, magrittr,
        plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse,
        VennDiagram
biocViews: ChIPSeq, HiC, Sequencing, Coverage
BiocType: Software
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/extraChIPs
git_branch: RELEASE_3_21
git_last_commit: 73770ee
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-16 00:37:44 UTC; biocbuild
Author: Stevie Pederson [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-8197-3303>)
Maintainer: Stevie Pederson <stephen.pederson.au@gmail.com>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:26:52 UTC; windows
Archs: x64
