Package: peakCombiner 1.3.0

Markus Muckenhuber

peakCombiner: The R package to curate and merge enriched genomic regions into consensus peak sets

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.

Authors:Markus Muckenhuber [aut, cre], Charlotte Soneson [aut], Michael Stadler [aut], Kathleen Sprouffske [aut], Novartis Biomedical Research [cph]

peakCombiner_1.3.0.tar.gz
peakCombiner_1.3.0.zip(r-4.7)peakCombiner_1.3.0.zip(r-4.6)peakCombiner_1.3.0.zip(r-4.5)
peakCombiner_1.3.0.tgz(r-4.6-any)peakCombiner_1.3.0.tgz(r-4.5-any)
peakCombiner_1.3.0.tar.gz(r-4.7-any)peakCombiner_1.3.0.tar.gz(r-4.6-any)
peakCombiner_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
peakCombiner/json (API)
NEWS

# Install 'peakCombiner' in R:
install.packages('peakCombiner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/novartis/peakcombiner/issues

Datasets:
  • syn_blacklist - Synthetic file with blacklisted regions for peakCombiner
  • syn_control_rep1_narrowPeak - Synthetic data set for control rep 1 sample in narrowPeak file format
  • syn_data_bed - Synthetic data set of genomic coordinates and meta data columns
  • syn_data_control01 - Synthetic data set of genomic coordinates and meta data columns filtered for control rep 1 sample
  • syn_data_granges - Synthetic data set of genomic coordinates and meta data columns
  • syn_data_tibble - Synthetic data set of genomic coordinates and meta data columns as tibble
  • syn_data_treatment01 - Synthetic data set of genomic coordinates and meta data columns filtered for treatment rep 1 sample
  • syn_sample_sheet - Synthetic sample sheet to load example data with peakCombiner
  • syn_treatment_rep1_narrowPeak - Synthetic data set for treatment rep 1 sample in narrowPeak file format

On BioConductor:peakCombiner-1.3.0(bioc 3.24)peakCombiner-1.2.0(bioc 3.23)

workflowsteppreprocessingchiponchip

5.26 score 6 stars 1 scripts 186 downloads 4 exports 37 dependencies

Last updated from:fadf0eafd3. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE200
linux-devel-x86_64OK243
source / vignettesOK312
linux-release-x86_64OK280
macos-release-arm64OK151
macos-oldrel-arm64OK138
windows-develOK158
windows-releaseOK157
windows-oldrelOK148
wasm-releaseOK172

Exports:centerExpandRegionscombineRegionsfilterRegionsprepareInputRegions

Dependencies:BiocGenericsbitbit64clicliprcpp11crayondplyrgenericsGenomicRangesglueherehmsIRangeslifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrrlangrprojrootS4VectorsSeqinfostringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

peakCombiner: The R package to curate and merge enriched genomic regions into consensus peak sets

Markus Muckenhuber, Charlotte Soneson, Michael Stadler, Kathleen Sprouffske

Rendered frompeakCombiner.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-08-18
Started: 2023-09-28

Readme and manuals

Help Manual

Help pageTopics
Modifies genomic regions by centering and then expanding themcenterExpandRegions
Control structure of peakCombiner data structurecheckDataStructure
collapse_summitscollapseSummits
Combine overlapping genomic regions from different samples to create a single set of consensus genomic regionscombineRegions
Update the center and score informationcrAddSummit
Separate genomic regions by coverage (disjoin) and filter input regionscrDisjoinFilter
Overlap genomic regions with original summits to remove false positivecrOverlapWithSummits
Recombine (reduce) input regionscrReduce
Calculate expansion value from median input region sizedefineExpansion
Apply user-defined filtering options to genomic regions.filterRegions
Prepare input data for peakCombiner packageprepareInputRegions
Synthetic file with blacklisted regions for peakCombinersyn_blacklist
Synthetic data set for control rep 1 sample in narrowPeak file formatsyn_control_rep1_narrowPeak
Synthetic data set of genomic coordinates and meta data columnssyn_data_bed
Synthetic data set of genomic coordinates and meta data columns filtered for control rep 1 samplesyn_data_control01
Synthetic data set of genomic coordinates and meta data columnssyn_data_granges
Synthetic data set of genomic coordinates and meta data columns as tibblesyn_data_tibble
Synthetic data set of genomic coordinates and meta data columns filtered for treatment rep 1 samplesyn_data_treatment01
Synthetic sample sheet to load example data with peakCombinersyn_sample_sheet
Synthetic data set for treatment rep 1 sample in narrowPeak file formatsyn_treatment_rep1_narrowPeak