Package: epiwraps 0.99.127

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_0.99.127.tar.gz
epiwraps_0.99.127.zip(r-4.7-any)epiwraps_0.99.127.zip(r-4.6-any)epiwraps_0.99.127.zip(r-4.5-any)
epiwraps_0.99.127.tgz(r-4.6-any)epiwraps_0.99.127.tgz(r-4.5-any)
epiwraps_0.99.127.tar.gz(r-4.7-any)epiwraps_0.99.127.tar.gz(r-4.6-any)
epiwraps_0.99.127.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epiwraps/json (API)

# 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

5.83 score 210 scripts 45 exports 113 dependencies

Last updated from:4347ea6696. Checks:4 NOTE, 4 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE175
linux-develERROR439
source / vignettesOK390
linux-releaseNOTE477
macos-releaseNOTE382
macos-oldrelNOTE353
windows-develERROR300
windows-releaseERROR364
windows-oldrelERROR357
wasm-releaseOK154

Exports:addAssayToESEannotateRegionsbam2bwbamChrChunkApplybreakStringsbwNormFactorscallPeaksclusterSignalMatricescolOverlapsEnrichmentSEestimateFragSizeexportNarrowPeaksformatGenomicDistfrag2bwfragSizesDistgetCovStatsgetNormFactorsgetSignalMatricesggSignalTracksimportBedlikeinjectmeltSignalsmergeSignalMatricesml2ESEpeakCountsFromBAMpeakCountsFromFragsplotCorFromCovStatsplotCovStatsplotEnrichedHeatmapsreduceRleListsreduceWithResplitregionCATregionOverlapsregionsToUpsetrenormalizeBordersrenormalizeSignalMatricesresizeMatrixscoreshowshowTrackInfosignal2MatrixtabixChrApplytileRleTSSenrichmentviews2Matrix

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIDelayedArraydigestdoParalleldplyredgeREnrichedHeatmapensembldbfarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpatchworkpbapplypillarpkgconfigpngProtGenericsR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraystatmodSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryaml

Generating bigwig tracks with bam2bw
Introduction | Many ways of compiling coverage | Example heatmaps created using different bigwig generation procedures | Working with fragment files as an input | Session information
Rendered frombam2bw.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2022-06-11

Visualizing signals in a single region
Plotting signals in a region | Merging signal from different tracks | Using an EnsDb object | Further track customization | Session info
Rendered fromsingleRegionPlot.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2024-01-23

Miscellaneous epiwraps functions
Getting read counts in regions of interest | Quality control | Coverage statistics | Fragment length distributions | TSS enrichment | Peak calling | Region merging | Region overlapping | Session information
Rendered frommisc.Rmdusingknitr::rmarkdown

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

Visualizing signals across many regions
Introduction | Reading signal in/around a set of regions | Extracting and manipulating signal matrices | Normalization | Plotting heatmaps | Color-scale trimming | Different colorscales for different tracks | Scaled regions | Heatmap rasterization | Sorting and clustering | Plotting aggregated signals | Visualizing DNAme and sparse signals | Session information
Rendered frommultiRegionPlot.Rmdusingknitr::rmarkdown

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

Normalizing genomic signals
Introduction | Applying normalization factors when generating the bigwig files | Obtaining normalization factors for a set of signal files | Normalization methods | Obtaining normalization factors from the signal matrices themselves | Session information
Rendered fromnormalization.Rmdusingknitr::rmarkdown

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

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
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
tabixChrApplytabixChrApply
tileRletileRle
TSSenrichmentTSSenrichment
views2Matrixviews2Matrix