peakCombiner
The R package to curate and merge enriched genomic regions into consensus peak sets
Bioconductor version: 3.24 · Package version: 1.3.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("peakCombiner")Details
| Maintainer | Markus Muckenhuber <markusmuckenhuber@gmx.at> |
| Author | Markus Muckenhuber [aut, cre] (ORCID: <https://orcid.org/0000-0003-1897-2329>), Charlotte Soneson [aut] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Michael Stadler [aut] (ORCID: <https://orcid.org/0000-0002-2269-4934>), Kathleen Sprouffske [aut] (ORCID: <https://orcid.org/0000-0001-7081-2598>), Novartis Biomedical Research [cph] |
| License | MIT + file LICENSE |
| URL | https://github.com/novartis/peakCombiner/, https://bioconductor.org/packages/peakCombiner |
| Bug Reports | https://github.com/novartis/peakCombiner/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChipOnChip, Preprocessing, Software, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/peakCombiner/ |
Citation
From within R, enter citation("peakCombiner"):
Markus Muckenhuber, Charlotte Soneson, Michael Stadler, Kathleen Sprouffske. peakCombiner: The R package to curate and merge enriched genomic regions into consensus peak sets. doi:10.18129/B9.bioc.peakCombiner, R package version 1.3.0, https://bioconductor.org/packages/peakCombiner.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the 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 (arm64) | peakCombiner_1.3.0.tgz |
| macOS binary (x86_64) | peakCombiner_1.3.0.tgz |
Dependencies
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
Suggests: testthat (>= 3.0.0), tidyverse, rmarkdown, styler, cli, lintr, rtracklayer, knitr, devtools, ggplot2, BiocStyle, BiocManager, usethis, utils, AnnotationHub, GenomeInfoDb