Package: epiwraps 0.99.120

Pierre-Luc Germain

epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

A set of wrappers to facilitate working with epigenomics data. Includes in particular wrappers for producing multitrack single-regions plots, enrichment heatmaps, bigwig generation, normalization, etc. The focus was put on a simple yet flexible interface.

Authors:Pierre-Luc Germain [cre, aut]

epiwraps_0.99.120.tar.gz
epiwraps_0.99.120.zip(r-4.7)epiwraps_0.99.120.zip(r-4.6)epiwraps_0.99.120.zip(r-4.5)
epiwraps_0.99.120.tgz(r-4.6-any)epiwraps_0.99.120.tgz(r-4.5-any)
epiwraps_0.99.120.tar.gz(r-4.7-any)epiwraps_0.99.120.tar.gz(r-4.6-any)
epiwraps_0.99.120.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
epiwraps/json (API)
NEWS

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

Bug tracker:https://github.com/ethz-ins/epiwraps/issues

Pkgdown/docs site:https://ethz-ins.github.io

Datasets:

On CRAN:

Conda:

epigeneticssequencingnormalizationvisualization

5.55 score 204 scripts 46 exports 160 dependencies

Last updated from:fd46fd6925. Checks:5 NOTE, 2 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE255
linux-devel-x86_64NOTE496
source / vignettesOK442
linux-release-x86_64NOTE597
macos-release-arm64NOTE498
macos-oldrel-arm64NOTE699
windows-develERROR412
windows-releaseERROR423
windows-oldrelERROR460
wasm-releaseOK191

Exports:addAssayToESEannotateRegionsbam2bwbamChrChunkApplybreakStringsbwNormFactorscallPeaksclusterSignalMatricescolOverlapsEnrichmentSEestimateFragSizeexportNarrowPeaksformatGenomicDistfrag2bwfragSizesDistgetCovStatsgetNormFactorsgetSignalMatricesggSignalTracksimportBedlikeinjectmeltSignalsmergeSignalMatricesml2ESEpeakCountsFromBAMpeakCountsFromFragsplotCorFromCovStatsplotCovStatsplotEnrichedHeatmapsplotSignalTracksreduceRleListsreduceWithResplitregionCATregionOverlapsregionsToUpsetrenormalizeBordersrenormalizeSignalMatricesresizeMatrixscoreshowshowTrackInfosignal2MatrixtabixChrApplytileRleTSSenrichmentviews2Matrix

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdoParalleldplyredgeREnrichedHeatmapensembldbevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesGetoptLongggplot2GlobalOptionsgluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslpatchworkpbapplypillarpkgconfigpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoshapesnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Generating bigwig tracks with bam2bw

Pierre-Luc Germain

Rendered frombam2bw.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-05-06
Started: 2022-06-11

Miscellaneous epiwraps functions

Pierre-Luc Germain

Rendered frommisc.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-05-06
Started: 2024-02-15

Visualizing signals across many regions

Pierre-Luc Germain

Rendered frommultiRegionPlot.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-05-06
Started: 2024-01-23

Normalizing genomic signals

Pierre-Luc Germain

Rendered fromnormalization.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-05-06
Started: 2024-04-29

Visualizing signals in a single region

Pierre-Luc Germain

Rendered fromsingleRegionPlot.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2026-05-19
Started: 2024-01-23

Readme and manuals

Help Manual

Help pageTopics
addAssayToESEaddAssayToESE
annotateRegionsannotateRegions
bam2bw: create a coverage bigwig file from an alignment bam file.bam2bw
bamChrChunkApplybamChrChunkApply
breakStringsbreakStrings
callPeakscallPeaks
clusterSignalMatrices: clusters the regions of a (set of) signal matrices.clusterSignalMatrices
colOverlapscolOverlaps
EnrichmentSE class and constructor.EnrichmentSE EnrichmentSE EnrichmentSE-class score,EnrichmentSE-method show,EnrichmentSE-method [,EnrichmentSE,ANY,ANY,ANY-method
estimateFragSizeestimateFragSize
Example DNAme data on some active gene bodiesexampleDNAme geneBodies
Example EnrichmentSE objectexampleESE
exportNarrowPeaksexportNarrowPeaks
formatGenomicDistformatGenomicDist
frag2bwfrag2bw
fragSizesDistfragSizesDist
getCovStatsgetCovStats
getEmpiricalFDRgetEmpiricalFDR
getNormFactors : estimate normalization factors from genomic signal filesbwNormFactors getNormFactors
getSignalMatricesgetSignalMatrices
ggSignalTracks: Plot genomic signal tracks with ggplot2ggSignalTracks
importBedlikeimportBedlike
Inject (insert) values at positions in a vectorinject
meltSignalsmeltSignals
mergeSignalMatrices: aggregates two or more signal matrices.mergeSignalMatrices
Creates an EnrichmentSE from a list of normalizedMatrix objectsml2ESE
peakCountsFromBAMpeakCountsFromBAM
peakCountsFromFragspeakCountsFromFrags
plotCorFromCovStatsplotCorFromCovStats
plotCovStatsplotCovStats
plotEnrichedHeatmaps: Plots heatmaps of signals around a set of regionsplotEnrichedHeatmaps
plotSignalTracksplotSignalTracks
reduceRleListsreduceRleLists
Merge regions, re-splitting large merges using local overlap minimareduceWithResplit
regionCATregionCAT
regionOverlapsregionOverlaps
regionsToUpsetregionsToUpset
renormalizeSignalMatricesrenormalizeBorders renormalizeSignalMatrices
resize a numeric matrix to given dimensionsresizeMatrix
showTrackInfoshowTrackInfo
signal2Matrix: reads the signals in/around a set of genomic regions.signal2Matrix
signalsAcrossSamplessignalsAcrossSamples
tabixChrApplytabixChrApply
tileRletileRle
TSSenrichmentTSSenrichment
views2Matrixviews2Matrix