extraChIPs

This is the released version of extraChIPs; for the devel version, see extraChIPs.

Additional functions for working with ChIP-Seq data

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DOI: 10.18129/B9.bioc.extraChIPs

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0001-8197-3303

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

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

Installation

To install this package, start R (version "4.5") 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")

Differential Signal Analysis (Fixed-Width Windows) HTML R Script

Differential Signal Analysis (Sliding Windows) HTML R Script

Range-Based Operations HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, Coverage, HiC, Sequencing, Software

Version 1.14.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 years)

License GPL-3

Depends BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 4.0.0), ggside (>= 0.4.0), Seqinfo, SummarizedExperiment(>= 1.39.1), tibble

Imports csaw, dplyr (>= 1.1.1), edgeR(>= 4.0), forcats, GenomeInfoDb, glue, ggrepel, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, vctrs

System Requirements

URL https://github.com/smped/extraChIPs

Bug Reports https://github.com/smped/extraChIPs/issues

Suggests apeglm, BiocStyle, SimpleUpset, covr, DESeq2, EnrichedHeatmap, GenomicAlignments, GenomicInteractions, Gviz, ggforce, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse, VennDiagram

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 extraChIPs_1.14.0.tar.gz

Windows Binary (x86_64) extraChIPs_1.13.2.zip

macOS Binary (x86_64) extraChIPs_1.14.0.tgz

macOS Binary (arm64) extraChIPs_1.14.0.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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