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compEpiTools (version 1.4.0)

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

1.4.0

License

GPL

Maintainer

Kamal Kishore

Last Published

February 15th, 2017

Functions in compEpiTools (1.4.0)

heatmapPlot

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

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

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

A GRanges method to define enhancers based on H3K4me1 peaks
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
simplifyGOterms

simplify a list of GO terms
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
makeGtfFromDb-methods

Utilities to transform a TxDb into a GTF file
stallingIndex

returns a list with average read count on TSS, gene body, and stalling index for a number of samples
GRanges2ucsc-methods

A GRanges method to convert ranges information into UCSC format
GRannotate-methods

Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
GRannotateSimple-methods

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

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

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

Identify putative long non coding RNAs (lncRNA)
getPromoterClass

Determining the CpG promoter class and the average CpG content
GRcoverage-methods

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

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

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

visualization of GRanges overlap
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
compEpiTools-package

Tools for computational epigenomics
GRsetwidth-methods

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

given a query and a subject GRanges returns a matrix of counts of subject in bins of query
palette2d

build a two dimensional color palette
heatmapData

Based on a list of GRanges, determine various kind of counts before displaying a heatmap
plotStallingIndex

Stalling Index plots