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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("compEpiTools")
AuthorMattia Pelizzola, Kamal Kishore
Bioconductor views Coverage GeneExpression GenomeAnnotation Sequencing Visualization
Date of publicationNone
MaintainerKamal Kishore <kamal.fartiyal84@gmail.com>
LicenseGPL
Version1.10.0

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...

Functions

compEpiTools Man page
compEpiTools-package Man page
countOverlapsInBins Man page
countOverlapsInBins,GRanges-method Man page
countOverlapsInBins-methods Man page
distanceFromTSS Man page
distanceFromTSS,GRanges-method Man page
distanceFromTSS-methods Man page
enhancers Man page
enhancers,GRanges-method Man page
enhancers-methods Man page
featuresLength Man page
featuresLength-methods Man page
featuresLength,TxDb-method Man page
findLncRNA Man page
getPromoterClass Man page
getPromoterClass-methods Man page
getPromoterClass,TxDb-method Man page
GR2fasta Man page
GR2fasta,GRanges-method Man page
GR2fasta-methods Man page
GRanges2ucsc Man page
GRanges2ucsc,GRanges-method Man page
GRanges2ucsc-methods Man page
GRangesInPromoters Man page
GRangesInPromoters,GRanges-method Man page
GRangesInPromoters-methods Man page
GRannotate Man page
GRannotate,GRanges-method Man page
GRannotate-methods Man page
GRannotateSimple Man page
GRannotateSimple,GRanges-method Man page
GRannotateSimple-methods Man page
GRbaseCoverage Man page
GRbaseCoverage,GRanges-method Man page
GRbaseCoverage-methods Man page
GRcoverage Man page
GRcoverage,GRanges-method Man page
GRcoverageInbins Man page
GRcoverageInbins,GRanges-method Man page
GRcoverageInbins-methods Man page
GRcoverage-methods Man page
GRcoverageSummit Man page
GRcoverageSummit,GRanges-method Man page
GRcoverageSummit-methods Man page
GRenrichment Man page
GRenrichment,GRanges-method Man page
GRenrichment-methods Man page
GRmidpoint Man page
GRmidpoint,GRanges-method Man page
GRmidpoint-methods Man page
GRsetwidth Man page
GRsetwidth,GRanges-method Man page
GRsetwidth-methods Man page
heatmapData Man page
heatmapPlot Man page
makeGtfFromDb Man page
makeGtfFromDb-methods Man page
makeGtfFromDb,TxDb-method Man page
matchEnhancers Man page
matchEnhancers,GRanges-method Man page
matchEnhancers-methods Man page
overlapOfGRanges Man page
overlapOfGRanges,GRanges-method Man page
overlapOfGRanges-methods Man page
palette2d Man page
plotStallingIndex Man page
simplifyGOterms Man page
stallingIndex Man page
topGOres Man page
TSS Man page
ucsc2GRanges Man page
unionMaxScore Man page
unionMaxScore,GRanges-method Man page
unionMaxScore-methods Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.