compEpiTools-package: Tools for computational epigenomics
In compEpiTools: Tools for computational epigenomics

Tools for computational epigenomics

The package offers the following functionalities, divided by topic

Counting reads in GRanges:

GRbaseCoverage: 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
GRcoverageInbins: same as GRcoverage but dividing each range in equally-sized bins
GRcoverageSummit: 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
countOverlapsInBins: given a query and a subject GRanges returns a matrix of counts of subject in bins of query
stallingIndex: computes the PolII stalling index based on number of ChIP-seq reads in promoter and genebody

Annotation of genomic regions:

TSS: based on a tXDb returns a GRanges with the TSS positions for all transcripts
distanceFromTSS: based on a GRanges, returnes the GRanges annotated with info about the closer TSS
GRangesInPromoters: based on a GRanges and a TxDb, subsets the GRanges to those regions overlapping with promoters
GRmidpoint: returns a GRanges containing the mid point of a GRanges
GRannotate: 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
makeGtfFromDb: utilities to transform a TranscriptDb into a GTF file

Functional annotation:

enhancers: a GRanges method to define enhancers based on H3K4me1 peaks
matchEnhancers: a GRanges method to match enhancers with putative targets sites (either TSS or TF-bound TSS)
topGOres: determines GeneOntology enriched terms for a set of gene ids
simplifyGOterms: simplify a list of GeneOntology terms based on the list of genes assigned to each GO term
findLncRNA: identify putative long non coding RNAs (lncRNA) based on ChIP-seq chromatin features and RNAseq data
getPromoterClass: determining the CpG promoter class and the average CpG content

Visualization:

heatmapData: Based on a list of GRanges, determine various kind of counts before displaying a heatmap
palette2d: build a two dimensional color palette
heatmapPlot: displays the heatmap based on the data from GRheatmapData
plotStallingIndex: plot the PolII stalling index

Other:

GR2fasta: A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome
overlapOfGRanges: given a list of GRanges, all pair-wise overlap are evaluated and the percentage of overlapping ranges is visualized in a heatmap
GRsetwidth: set the width of a GRanges based on the mid point of each region
unionMaxScore: GRanges method to perform union of peaks keeping the pvalue of the most significant peak
GRanges2ucsc: a GRanges method to convert ranges information into UCSC format
ucsc2GRanges: convert UCSC-formatted genomic positions into a GRanges