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Bioconductor - extraChIPs (development version)

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 (3.22)

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: 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")

# 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

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

browseVignettes("extraChIPs")
Details biocViews ChIPSeq, Coverage, HiC, Sequencing, Software Version 1.13.2 In Bioconductor since BioC 3.15 (R-4.2) (3 years) License GPL-3 Depends BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0), ggside (>= 0.3.1), SummarizedExperiment, tibble Imports csaw, dplyr (>= 1.1.1), edgeR(>= 4.0), forcats, GenomeInfoDb, glue, ggrepel, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, Seqinfo, scales, stats, stringr, tidyr, tidyselect, vctrs System Requirements URL https://github.com/smped/extraChIPs Bug Reports https://github.com/smped/extraChIPs/issues See More Suggests apeglm, BiocStyle, ComplexUpset, 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 Build Report Build Report Package Archives

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

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