DOI: 10.18129/B9.bioc.extraChIPs  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see extraChIPs.

Additional functions for working with ChIP-Seq data

Bioconductor version: 3.17

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.

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 Signal Analysis (Fixed-Width Windows)
HTML R Script Differential Signal Analysis (Sliding Windows)
HTML R Script Range-Based Operations
PDF   Reference Manual
Text   NEWS


biocViews ChIPSeq, Coverage, HiC, Sequencing, Software
Version 1.4.6
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License GPL-3
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
URL https://github.com/smped/extraChIPs
BugReports https://github.com/smped/extraChIPs/issues
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Source Package extraChIPs_1.4.6.tar.gz
Windows Binary extraChIPs_1.4.6.zip
macOS Binary (x86_64) extraChIPs_1.4.6.tgz
macOS Binary (arm64) extraChIPs_1.4.6.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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