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 (3.24)
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]
Maintainer: Stevie Pederson <stephen.pederson.au at gmail.com>
citation("extraChIPs")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Coverage, HiC, Sequencing, Software |
| Version | 1.17.4 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | extraChIPs_1.17.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | extraChIPs_1.17.4.tgz |
| macOS Binary (sonoma-arm64) | extraChIPs_1.17.4.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 |