peakCombiner
This is the released version of peakCombiner; for the devel version, see peakCombiner.
The R package to curate and merge enriched genomic regions into consensus peak sets
Bioconductor version: Release (3.22)
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")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | peakCombiner_1.0.0.tgz |
| macOS Binary (arm64) | peakCombiner_1.0.0.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 |