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.

AuthorMattia Pelizzola, Kamal Kishore
Date of publicationNone
MaintainerKamal Kishore <kamal.fartiyal84@gmail.com>
LicenseGPL
Version1.8.0

View on Bioconductor

Man pages

compEpiTools-package: Tools for computational epigenomics

countOverlapsInBins-methods: given a query and a subject GRanges returns a matrix of...

distanceFromTSS-methods: Returns the GRanges annotated with info about the closer TSS

enhancers: A GRanges method to define enhancers based on H3K4me1 peaks

findLncRNA: Identify putative long non coding RNAs (lncRNA)

getPromoterClass-methods: Determining the CpG promoter class and the average CpG...

GR2fasta-methods: A GRanges method to extract and write to the disk a fasta...

GRanges2ucsc-methods: A GRanges method to convert ranges information into UCSC...

GRangesInPromoters-methods: Based on a GRanges and a TxDb, subsets the GRanges to those...

GRannotate-methods: Based on a GRanges and a TxDb, returns the GRanges with a...

GRannotateSimple: a GRanges method to split a GRanges in three GRanges:...

GRbaseCoverage-methods: Based on a GRanges and a BAM file, returns a list of base...

GRcoverage-methods: based on a GRanges and a BAM file, returns the total coverage...

GRcoverageSummit-methods: Based on a GRanges and a BAM file, returns a GRanges with the...

GRenrichment-methods: Determines the enrichment over a set of genomic regions given...

GRmidpoint-methods: Returns a GRanges containing the mid point of a GRanges

GRsetwidth: Set the width of a GRanges based on the mid point of each...

heatmapData: Based on a list of GRanges, determine various kind of counts...

heatmapPlot: displays the heatmap based on the data from heatmapData

makeGtfFromDb: Utilities to transform a TxDb into a GTF file

matchEnhancers: GRanges method to match enhancers with putative targets sites

overlapOfGRanges-methods: visualization of GRanges overlap

palette2d: build a two dimensional color palette

plotStallingIndex: Stalling Index plots

simplifyGOterms: simplify a list of GO terms

stallingIndex: returns a list with average read count on TSS, gene body, and...

topGOres: determines GeneOntology (GO) enriched terms for a set of...

TSS: based on a TxDb returns a GRanges with the TSS positions for...

ucsc2GRanges: Convert UCSC-formatted genomic positions into a GRanges

unionMaxScore-methods: GRanges method to perform union of peaks keeping the score of...

Files in this package

compEpiTools/DESCRIPTION
compEpiTools/NAMESPACE
compEpiTools/NEWS
compEpiTools/R
compEpiTools/R/GR2fasta.R compEpiTools/R/GRanges2ucsc.R compEpiTools/R/GRangesInPromoters.R compEpiTools/R/GRannotate.R compEpiTools/R/GRannotateSimple.R compEpiTools/R/GRbaseCoverage.R compEpiTools/R/GRcoverage.R compEpiTools/R/GRcoverageInbins.R compEpiTools/R/GRcoverageSummit.R compEpiTools/R/GRenrichment.R compEpiTools/R/GRmidpoint.R compEpiTools/R/GRsetwidth.R compEpiTools/R/TSS.R compEpiTools/R/countOverlapsInBins.R compEpiTools/R/distanceFromTSS.R compEpiTools/R/enhancers.R compEpiTools/R/featuresLength.R compEpiTools/R/findLncRNA.R compEpiTools/R/getPromoterClass.R compEpiTools/R/heatmapData.R compEpiTools/R/heatmapPlot.R compEpiTools/R/makeGtfFromDb.R compEpiTools/R/matchEnhancers.R compEpiTools/R/overlapOfGRanges.R compEpiTools/R/palette2d.R compEpiTools/R/plotStallingIndex.R compEpiTools/R/simplifyGOterms.R compEpiTools/R/stallingIndex.R compEpiTools/R/topGOres.R compEpiTools/R/ucsc2GRanges.R compEpiTools/R/unionMaxScore.R
compEpiTools/build
compEpiTools/build/vignette.rds
compEpiTools/inst
compEpiTools/inst/CITATION
compEpiTools/inst/doc
compEpiTools/inst/doc/compEpiTools.R
compEpiTools/inst/doc/compEpiTools.pdf
compEpiTools/inst/doc/compEpiTools.rnw
compEpiTools/inst/extdata
compEpiTools/inst/extdata/CGIgr_mm9.Rdata
compEpiTools/inst/extdata/H3K4me1.bam
compEpiTools/inst/extdata/H3K4me1.bam.bai
compEpiTools/inst/extdata/H3K4me1GR.Rda
compEpiTools/inst/extdata/H3K4me3.bam
compEpiTools/inst/extdata/H3K4me3.bam.bai
compEpiTools/inst/extdata/H3K4me3GR.Rda
compEpiTools/inst/extdata/Pol2.bam
compEpiTools/inst/extdata/Pol2.bam.bai
compEpiTools/inst/extdata/Pol2GR.Rda
compEpiTools/man
compEpiTools/man/GR2fasta-methods.Rd compEpiTools/man/GRanges2ucsc-methods.Rd compEpiTools/man/GRangesInPromoters-methods.Rd compEpiTools/man/GRannotate-methods.Rd compEpiTools/man/GRannotateSimple.Rd compEpiTools/man/GRbaseCoverage-methods.Rd compEpiTools/man/GRcoverage-methods.Rd compEpiTools/man/GRcoverageSummit-methods.Rd compEpiTools/man/GRenrichment-methods.Rd compEpiTools/man/GRmidpoint-methods.Rd compEpiTools/man/GRsetwidth.Rd compEpiTools/man/TSS.Rd compEpiTools/man/compEpiTools-package.Rd compEpiTools/man/countOverlapsInBins-methods.Rd compEpiTools/man/distanceFromTSS-methods.Rd compEpiTools/man/enhancers.Rd compEpiTools/man/findLncRNA.Rd compEpiTools/man/getPromoterClass-methods.Rd compEpiTools/man/heatmapData.Rd compEpiTools/man/heatmapPlot.Rd compEpiTools/man/makeGtfFromDb.Rd compEpiTools/man/matchEnhancers.Rd compEpiTools/man/overlapOfGRanges-methods.Rd compEpiTools/man/palette2d.Rd compEpiTools/man/plotStallingIndex.Rd compEpiTools/man/simplifyGOterms.Rd compEpiTools/man/stallingIndex.Rd compEpiTools/man/topGOres.Rd compEpiTools/man/ucsc2GRanges.Rd compEpiTools/man/unionMaxScore-methods.Rd
compEpiTools/vignettes
compEpiTools/vignettes/compEpiTools.rnw

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