Package: extraChIPs
Version: 1.4.6
Title: Additional functions for working with ChIP-Seq data
Authors@R: person("Stephen", "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 included.
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 (>= 3.4.0),
        SummarizedExperiment, tibble
Imports: BiocIO, broom, ComplexUpset, csaw, dplyr (>= 1.1.0), edgeR,
        EnrichedHeatmap, forcats, GenomeInfoDb, GenomicInteractions,
        ggforce, ggrepel, ggside, glue, grDevices, grid, Gviz,
        InteractionSet, IRanges, limma, matrixStats, methods,
        patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer,
        S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils,
        vctrs, VennDiagram
Suggests: BiocStyle, covr, cqn, harmonicmeanp, here, knitr, magrittr,
        plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse
biocViews: ChIPSeq, HiC, Sequencing, Coverage
BiocType: Software
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/extraChIPs
git_branch: RELEASE_3_17
git_last_commit: 099625f
git_last_commit_date: 2023-07-08
Date/Publication: 2023-07-09
NeedsCompilation: yes
Packaged: 2023-07-10 06:21:56 UTC; biocbuild
Author: Stephen Pederson [aut, cre] (<https://orcid.org/0000-0001-8197-3303>)
Maintainer: Stephen Pederson <stephen.pederson.au@gmail.com>
Built: R 4.3.1; aarch64-apple-darwin20; 2023-07-13 14:34:14 UTC; unix
