extraChIPs

DOI: 10.18129/B9.bioc.extraChIPs  

Additional functions for working with ChIP-Seq data

Bioconductor version: Release (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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("extraChIPs")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("extraChIPs")

 

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

Details

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
LinkingTo
Suggests	BiocStyle, covr, knitr, plyranges, rmarkdown, testthat (>= 3.0.0), tidyverse
SystemRequirements
Enhances
URL	https://github.com/steveped/extraChIPs
BugReports	https://github.com/steveped/extraChIPs/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive