Package: compEpiTools 1.41.0

Mattia Furlan

compEpiTools: Tools for computational epigenomics

Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.

Authors:Mattia Pelizzola [aut], Kamal Kishore [aut], Mattia Furlan [ctb, cre]

compEpiTools_1.41.0.tar.gz
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compEpiTools.pdf |compEpiTools.html✨
compEpiTools/json (API)
NEWS

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

Peer review:

On BioConductor:compEpiTools-1.39.0(bioc 3.20)compEpiTools-1.38.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressionsequencingvisualizationgenomeannotationcoverage

3.30 score 6 scripts 225 downloads 31 exports 159 dependencies

Last updated 20 days agofrom:87788a370c. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 31 2024

Exports:countOverlapsInBinsdistanceFromTSSenhancersfeaturesLengthfindLncRNAgetPromoterClassGR2fastaGRanges2ucscGRangesInPromotersGRannotateGRannotateSimpleGRbaseCoverageGRcoverageGRcoverageInbinsGRcoverageSummitGRenrichmentGRmidpointGRsetwidthheatmapDataheatmapPlotmakeGtfFromDbmatchEnhancersoverlapOfGRangespalette2dplotStallingIndexsimplifyGOtermsstallingIndextopGOresTSSucsc2GRangesunionMaxScore

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGO.dbgplotsgraphgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmamagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmemoisemethylPipemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextopGOUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

compEpiTools

Rendered fromcompEpiTools.rnwusingknitr::knitron Oct 30 2024.

Last update: 2015-06-08
Started: 2014-08-27

Readme and manuals

Help Manual

Help pageTopics
Tools for computational epigenomicscompEpiTools-package compEpiTools
given a query and a subject GRanges returns a matrix of counts of subject in bins of querycountOverlapsInBins countOverlapsInBins,GRanges-method countOverlapsInBins-methods
Returns the GRanges annotated with info about the closer TSSdistanceFromTSS distanceFromTSS,GRanges-method distanceFromTSS-methods
A GRanges method to define enhancers based on H3K4me1 peaksenhancers enhancers,GRanges-method enhancers-methods
Identify putative long non coding RNAs (lncRNA)findLncRNA
Determining the CpG promoter class and the average CpG contentgetPromoterClass getPromoterClass,TxDb-method getPromoterClass-methods
A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genomeGR2fasta GR2fasta,GRanges-method GR2fasta-methods
A GRanges method to convert ranges information into UCSC formatGRanges2ucsc GRanges2ucsc,GRanges-method GRanges2ucsc-methods
Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promotersGRangesInPromoters GRangesInPromoters,GRanges-method GRangesInPromoters-methods
Based on a GRanges and a TxDb, returns the GRanges with a series of annotationsGRannotate GRannotate,GRanges-method GRannotate-methods
a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenicGRannotateSimple GRannotateSimple,GRanges-method GRannotateSimple-methods
Based on a GRanges and a BAM file, returns a list of base coverage vectors for each rangeGRbaseCoverage GRbaseCoverage,GRanges-method GRbaseCoverage-methods
based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.GRcoverage GRcoverage,GRanges-method GRcoverage-methods GRcoverageInbins GRcoverageInbins,GRanges-method GRcoverageInbins-methods
Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each rangeGRcoverageSummit GRcoverageSummit,GRanges-method GRcoverageSummit-methods
Determines the enrichment over a set of genomic regions given two BAM filesGRenrichment GRenrichment,GRanges-method GRenrichment-methods
Returns a GRanges containing the mid point of a GRangesGRmidpoint GRmidpoint,GRanges-method GRmidpoint-methods
Set the width of a GRanges based on the mid point of each regionGRsetwidth GRsetwidth,GRanges-method GRsetwidth-methods
Based on a list of GRanges, determine various kind of counts before displaying a heatmapheatmapData
displays the heatmap based on the data from heatmapDataheatmapPlot
Utilities to transform a TxDb into a GTF filefeaturesLength featuresLength,TxDb-method featuresLength-methods makeGtfFromDb makeGtfFromDb,TxDb-method makeGtfFromDb-methods
GRanges method to match enhancers with putative targets sitesmatchEnhancers matchEnhancers,GRanges-method matchEnhancers-methods
visualization of GRanges overlapoverlapOfGRanges overlapOfGRanges,GRanges-method overlapOfGRanges-methods
build a two dimensional color palettepalette2d
Stalling Index plotsplotStallingIndex
simplify a list of GO termssimplifyGOterms
returns a list with average read count on TSS, gene body, and stalling index for a number of samplesstallingIndex
determines GeneOntology (GO) enriched terms for a set of Entrez gene idstopGOres
based on a TxDb returns a GRanges with the TSS positions for all transcriptsTSS
Convert UCSC-formatted genomic positions into a GRangesucsc2GRanges
GRanges method to perform union of peaks keeping the score of the most significant peakunionMaxScore unionMaxScore,GRanges-method unionMaxScore-methods