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compEpiTools (version 1.0.3)

Tools for computational epigenomics

Description

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.

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Version

Version

1.0.3

License

GPL

Maintainer

Kamal Kishore

Last Published

February 15th, 2017

Functions in compEpiTools (1.0.3)

GRangesInPromoters-methods

Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters
compEpiTools-package

Tools for computational epigenomics
countOverlapsInBins-methods

given a query and a subject GRanges returns a matrix of counts of subject in bins of query
heatmapPlot

displays the heatmap based on the data from heatmapData
makeGtfFromDb-methods

Utilities to transform a TxDb into a GTF file
GRannotate-methods

Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
palette2d

build a two dimensional color palette
plotStallingIndex

Stalling Index plots
distanceFromTSS-methods

Returns the GRanges annotated with info about the closer TSS
GRanges2ucsc-methods

A GRanges method to convert ranges information into UCSC format
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
heatmapData

Based on a list of GRanges, determine various kind of counts before displaying a heatmap
GRsetwidth-methods

Set the width of a GRanges based on the mid point of each region
matchEnhancers-methods

GRanges method to match enhancers with putative targets sites
overlapOfGRanges-methods

visualization of GRanges overlap
enhancers-methods

A GRanges method to define enhancers based on H3K4me1 peaks
GRenrichment-methods

Determines the enrichment over a set of genomic regions given two BAM files
GRmidpoint-methods

Returns a GRanges containing the mid point of a GRanges
ucsc2GRanges

Convert UCSC-formatted genomic positions into a GRanges
unionMaxScore-methods

GRanges method to perform union of peaks keeping the score of the most significant peak
GRcoverage-methods

based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageSummit-methods

Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range
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
findLncRNA

Identify putative long non coding RNAs (lncRNA)
GRannotateSimple-methods

a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic
GRbaseCoverage-methods

Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range
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
getPromoterClass

Determining the CpG promoter class and the average CpG content