peakCombiner
This is the development version of peakCombiner; for the stable release version, see peakCombiner.
The R package to curate and merge enriched genomic regions into consensus peak sets
Bioconductor version: Development (3.24)
peakCombiner, a fully R based, user-friendly, transparent, and customizable tool that allows even novice R users to create a high-quality consensus peak list. The modularity of its functions allows an easy way to optimize input and output data. A broad range of accepted input data formats can be used to create a consensus peak set that can be exported to a file or used as the starting point for most downstream peak analyses.
Author: Markus Muckenhuber [aut, cre]
, Charlotte Soneson [aut]
, Michael Stadler [aut]
, Kathleen Sprouffske [aut]
, Novartis Biomedical Research [cph]
Maintainer: Markus Muckenhuber <markusmuckenhuber at gmx.at>
citation("peakCombiner")):
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("peakCombiner")
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("peakCombiner")| peakCombiner | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChipOnChip, Preprocessing, Software, WorkflowStep |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | tidyr, dplyr (>= 1.1.2), IRanges, GenomicRanges, tidyselect, purrr, readr (>= 2.1.2), tibble (>= 3.2.1), rlang, stringr, here, stats, Seqinfo |
| System Requirements | |
| URL | https://github.com/novartis/peakCombiner/ https://bioconductor.org/packages/peakCombiner |
| Bug Reports | https://github.com/novartis/peakCombiner/issues |
See More
| Suggests | testthat (>= 3.0.0), tidyverse, rmarkdown, styler, cli, lintr, rtracklayer, knitr, devtools, ggplot2, BiocStyle, BiocManager, usethis, utils, AnnotationHub, GenomeInfoDb |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | peakCombiner_1.3.0.tar.gz |
| Windows Binary (x86_64) | peakCombiner_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | peakCombiner_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | peakCombiner_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/peakCombiner |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/peakCombiner |
| Bioc Package Browser | https://code.bioconductor.org/browse/peakCombiner/ |
| Package Short Url | https://bioconductor.org/packages/peakCombiner/ |
| Package Downloads Report | Download Stats |