extraChIPs

DOI: 10.18129/B9.bioc.extraChIPs    

Additional functions for working with ChIP-Seq data

Bioconductor version: Release (3.15)

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 implemented.

Author: Stephen Pederson [aut, cre]

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

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

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 1.0.4
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License GPL-3
Depends BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2, SummarizedExperiment, tibble
Imports BiocIO, broom, ComplexUpset, csaw, dplyr, edgeR, EnrichedHeatmap, forcats, GenomeInfoDb, GenomicInteractions, ggforce, ggrepel, ggside, glue, grDevices, grid, Gviz, InteractionSet, IRanges, limma, methods, 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_1.0.4.tar.gz
Windows Binary extraChIPs_1.0.4.zip
macOS Binary (x86_64) extraChIPs_1.0.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/extraChIPs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/extraChIPs
Package Short Url https://bioconductor.org/packages/extraChIPs/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive

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