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extraChIPs
This is thereleased version of extraChIPs; for the devel version, seeextraChIPs.
Additional functions for working with ChIP-Seq data
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: 0000-0001-8197-3303
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")BiocManager::install("extraChIPs")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq,Coverage,HiC,Sequencing,Software |
| Version | 1.14.2 |
| 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 |
See More
| 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 | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | extraChIPs_1.14.2.tar.gz |
| Windows Binary (x86_64) | extraChIPs_1.14.1.zip (64-bit only) |
| macOS Binary (x86_64) | extraChIPs_1.14.2.tgz |
| macOS Binary (arm64) | extraChIPs_1.14.2.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.22 | Source Archive |