Tools for computational epigenomics


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Documentation for package ‘compEpiTools’ version 1.41.0

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compEpiTools-package Tools for computational epigenomics
compEpiTools Tools for computational epigenomics
countOverlapsInBins given a query and a subject GRanges returns a matrix of counts of subject in bins of query
countOverlapsInBins-method given a query and a subject GRanges returns a matrix of counts of subject in bins of query
countOverlapsInBins-methods given a query and a subject GRanges returns a matrix of counts of subject in bins of query
distanceFromTSS Returns the GRanges annotated with info about the closer TSS
distanceFromTSS-method Returns the GRanges annotated with info about the closer TSS
distanceFromTSS-methods Returns the GRanges annotated with info about the closer TSS
enhancers A GRanges method to define enhancers based on H3K4me1 peaks
enhancers-method A GRanges method to define enhancers based on H3K4me1 peaks
enhancers-methods A GRanges method to define enhancers based on H3K4me1 peaks
featuresLength Utilities to transform a TxDb into a GTF file
featuresLength-method Utilities to transform a TxDb into a GTF file
featuresLength-methods Utilities to transform a TxDb into a GTF file
findLncRNA Identify putative long non coding RNAs (lncRNA)
getPromoterClass Determining the CpG promoter class and the average CpG content
getPromoterClass-method Determining the CpG promoter class and the average CpG content
getPromoterClass-methods Determining the CpG promoter class and the average CpG content
GR2fasta A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome
GR2fasta-method A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome
GR2fasta-methods A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome
GRanges2ucsc A GRanges method to convert ranges information into UCSC format
GRanges2ucsc-method A GRanges method to convert ranges information into UCSC format
GRanges2ucsc-methods A GRanges method to convert ranges information into UCSC format
GRangesInPromoters Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters
GRangesInPromoters-method Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters
GRangesInPromoters-methods Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters
GRannotate Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
GRannotate-method Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
GRannotate-methods Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
GRannotateSimple a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic
GRannotateSimple-method a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic
GRannotateSimple-methods a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic
GRbaseCoverage Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range
GRbaseCoverage-method Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range
GRbaseCoverage-methods Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range
GRcoverage based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverage-method based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverage-methods based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageInbins based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageInbins-method based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageInbins-methods based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageSummit Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range
GRcoverageSummit-method Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range
GRcoverageSummit-methods Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range
GRenrichment Determines the enrichment over a set of genomic regions given two BAM files
GRenrichment-method Determines the enrichment over a set of genomic regions given two BAM files
GRenrichment-methods Determines the enrichment over a set of genomic regions given two BAM files
GRmidpoint Returns a GRanges containing the mid point of a GRanges
GRmidpoint-method Returns a GRanges containing the mid point of a GRanges
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 region
GRsetwidth-method Set the width of a GRanges based on the mid point of each region
GRsetwidth-methods Set the width of a GRanges based on the mid point of each region
heatmapData Based on a list of GRanges, determine various kind of counts before displaying a heatmap
heatmapPlot displays the heatmap based on the data from heatmapData
makeGtfFromDb Utilities to transform a TxDb into a GTF file
makeGtfFromDb-method Utilities to transform a TxDb into a GTF file
makeGtfFromDb-methods Utilities to transform a TxDb into a GTF file
matchEnhancers GRanges method to match enhancers with putative targets sites
matchEnhancers-method GRanges method to match enhancers with putative targets sites
matchEnhancers-methods GRanges method to match enhancers with putative targets sites
overlapOfGRanges visualization of GRanges overlap
overlapOfGRanges-method visualization of GRanges overlap
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 stalling index for a number of samples
topGOres determines GeneOntology (GO) enriched terms for a set of Entrez gene ids
TSS based on a TxDb returns a GRanges with the TSS positions for all transcripts
ucsc2GRanges Convert UCSC-formatted genomic positions into a GRanges
unionMaxScore GRanges method to perform union of peaks keeping the score of the most significant peak
unionMaxScore-method GRanges method to perform union of peaks keeping the score of the most significant peak
unionMaxScore-methods GRanges method to perform union of peaks keeping the score of the most significant peak