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This is the development version of extraChIPs; for the stable release version, see extraChIPs.
Bioconductor version: Development (3.16)
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 visualisatino of results. Coercion to tibble objects is also included.
Author: Stephen Pederson [aut, cre]
Maintainer: Stephen Pederson <stephen.pederson.au at gmail.com>
Citation (from within R,
enter citation("extraChIPs")
):
To install this package, start R (version "4.2") 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.
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 |
Reference Manual | ||
Text | NEWS |
biocViews | ChIPSeq, Coverage, HiC, Sequencing, Software |
Version | 1.1.0 |
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, csaw, dplyr, edgeR, EnrichedHeatmap, forcats, GenomeInfoDb, GenomicInteractions, ggrepel, ggside, glue, grDevices, Gviz, InteractionSet, IRanges, limma, methods, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, scatterpie, stats, stringr, tidyr, tidyselect, utils, vctrs |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | extraChIPs_1.1.0.tar.gz |
Windows Binary | extraChIPs_1.1.0.zip |
macOS 10.13 (High Sierra) | extraChIPs_1.1.0.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 |
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