Tools for computational epigenomics

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Documentation for package ‘compEpiTools’ version 1.41.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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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