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extraChIPs

This is the development version of extraChIPs; for the stable release version, see extraChIPs.

Additional functions for working with ChIP-Seq data


Bioconductor version: Development (3.19)

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.

Author: Stevie Pederson [aut, cre]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("extraChIPs")

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

Documentation

Reference Manual PDF

Details

biocViews ChIPSeq, Coverage, HiC, Sequencing, Software
Version 1.7.7
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
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, GenomicInteractions, ggforce, ggrepel, glue, grDevices, grid, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram
System Requirements
URL https://github.com/smped/extraChIPs
Bug Reports https://github.com/smped/extraChIPs/issues
See More
Suggests BiocStyle, covr, cqn, DESeq2, EnrichedHeatmap, Gviz, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me motifTestR, transmogR
Links To Me
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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