DOI: 10.18129/B9.bioc.extraChIPs  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see extraChIPs.

Additional functions for working with ChIP-Seq data

Bioconductor version: 3.16

This package builds on existing tools and adds some simple but extremely useful capabilities for working with 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.

Author: Stephen Pederson [aut, cre]

Maintainer: Stephen Pederson <stephen.pederson.au at gmail.com>

Citation (from within R, enter citation("extraChIPs")):


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HTML R Script Differential Binding Analysis
HTML R Script Range-Based Operations
PDF   Reference Manual
Text   NEWS


biocViews ChIPSeq, Coverage, HiC, Sequencing, Software
Version 1.2.4
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
License GPL-3
Depends BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.4.0), SummarizedExperiment, tibble
Imports BiocIO, broom, ComplexUpset, csaw, dplyr, edgeR, EnrichedHeatmap, forcats, GenomeInfoDb, GenomicInteractions, ggforce, ggrepel, ggside, glue, grDevices, grid, Gviz, InteractionSet, IRanges, limma, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram
Suggests BiocStyle, covr, knitr, plyranges, rmarkdown, testthat (>= 3.0.0), tidyverse
URL https://github.com/steveped/extraChIPs
BugReports https://github.com/steveped/extraChIPs/issues
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Source Package extraChIPs_1.2.4.tar.gz
Windows Binary extraChIPs_1.2.4.zip
macOS Binary (x86_64) extraChIPs_1.2.4.tgz
macOS Binary (arm64) extraChIPs_1.2.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/extraChIPs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/extraChIPs
Bioc Package Browser https://code.bioconductor.org/browse/extraChIPs/
Package Short Url https://bioconductor.org/packages/extraChIPs/
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