compEpiTools: Tools for computational epigenomics

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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.

Author
Mattia Pelizzola, Kamal Kishore
Date of publication
None
Maintainer
Kamal Kishore <kamal.fartiyal84@gmail.com>
License
GPL
Version
1.8.0

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