DESCRIPTION

Package: extraChIPs
Version: 1.9.6
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:
  BiocIO,
  broom,
  ComplexUpset,
  csaw,
  dplyr (>= 1.1.1),
  edgeR (>= 4.0),
  forcats,
  GenomeInfoDb,
  GenomicAlignments,
  GenomicInteractions,
  ggforce,
  ggrepel,
  glue,
  grDevices,
  grid,
  InteractionSet,
  IRanges,
  matrixStats,
  methods,
  patchwork,
  RColorBrewer,
  rlang,
  Rsamtools,
  rtracklayer,
  S4Vectors,
  scales,
  stats,
  stringr,
  tidyr,
  tidyselect,
  utils,
  vctrs,
  VennDiagram
Suggests: 
  apeglm,
  BiocStyle,
  covr,
  DESeq2,
  EnrichedHeatmap,
  Gviz,
  harmonicmeanp,
  here,
  knitr,
  limma,
  magrittr,
  plyranges,
  quantro,
  rmarkdown,
  testthat (>= 3.0.0),
  tidyverse
biocViews: ChIPSeq, HiC, Sequencing, Coverage
BiocType: Software
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)  
RoxygenNote: 7.3.2
Config/testthat/edition: 3