matchEnhancers-methods
(Package: compEpiTools) :
GRanges method to match enhancers with putative targets sites
GRanges method to match enhancers with putative targets sites (either TSS or TF-bound TSS)
● Data Source:
BioConductor
● Keywords: methods
● Alias: matchEnhancers, matchEnhancers,GRanges-method, matchEnhancers-methods
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given a list of GRanges, all pair-wise overlap are evaluated and the percentage of overlapping ranges is visualized in a heatmap
● Data Source:
BioConductor
● Keywords: methods
● Alias: overlapOfGRanges, overlapOfGRanges,GRanges-method, overlapOfGRanges-methods
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palette2d
(Package: compEpiTools) :
build a two dimensional color palette
build a two dimensional color palette
● Data Source:
BioConductor
● Keywords:
● Alias: palette2d
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generates the plot from the output of the stallingIndex function. The plot has 3 panels: Stalling Index, TSS and gene body
● Data Source:
BioConductor
● Keywords:
● Alias: plotStallingIndex
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simplify a list of GeneOntology terms based on the list of genes assigned to each GO term
● Data Source:
BioConductor
● Keywords:
● Alias: simplifyGOterms
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stallingIndex
(Package: compEpiTools) :
returns a list with average read count on TSS, gene body, and
based on a TxDb, and a list of Pol2 ChIP-seq samples with a GRange corresponding to the peak call, returns a list whose elements contain the stalling index and average read count on TSS and gene body for a user-defined list of genes
● Data Source:
BioConductor
● Keywords:
● Alias: stallingIndex
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topGOres
(Package: compEpiTools) :
determines GeneOntology (GO) enriched terms for a set of Entrez
determines GeneOntology (GO) enriched terms for a set of Entrez gene ids
● Data Source:
BioConductor
● Keywords:
● Alias: topGOres
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ucsc2GRanges
(Package: compEpiTools) :
Convert UCSC-formatted genomic positions into a GRanges
Convert UCSC-formatted genomic positions to a GRanges object
● Data Source:
BioConductor
● Keywords:
● Alias: ucsc2GRanges
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unionMaxScore-methods
(Package: compEpiTools) :
GRanges method to perform union of peaks keeping the score of the
the union between two GRanges associated to scores is performed, and the most significant score for the overlapping regions is returned
● Data Source:
BioConductor
● Keywords: methods
● Alias: unionMaxScore, unionMaxScore,GRanges-method, unionMaxScore-methods
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GR2fasta-methods
(Package: compEpiTools) :
A GRanges method to extract and write to the disk a fasta file
Given a GRanges and a reference genome returns the sequences for all the ranges as in fasta format.
● Data Source:
BioConductor
● Keywords: methods
● Alias: GR2fasta, GR2fasta,GRanges-method, GR2fasta-methods
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providing 
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