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 (3.21)
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:
Maintainer: Stevie Pederson <stephen.pederson.au at gmail.com>
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")| 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 |
Details
| biocViews | ChIPSeq, Coverage, HiC, Sequencing, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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, GenomicAlignments, 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 | apeglm, BiocStyle, covr, 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 | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | extraChIPs_1.11.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/extraChIPs/ |
| Package Short Url | https://bioconductor.org/packages/extraChIPs/ |
| Package Downloads Report | Download Stats |