Man pages for Bioconductor-mirror/compEpiTools
Tools for computational epigenomics

compEpiTools-packageTools for computational epigenomics
countOverlapsInBins-methodsgiven a query and a subject GRanges returns a matrix of...
distanceFromTSS-methodsReturns the GRanges annotated with info about the closer TSS
enhancersA GRanges method to define enhancers based on H3K4me1 peaks
findLncRNAIdentify putative long non coding RNAs (lncRNA)
getPromoterClass-methodsDetermining the CpG promoter class and the average CpG...
GR2fasta-methodsA GRanges method to extract and write to the disk a fasta...
GRanges2ucsc-methodsA GRanges method to convert ranges information into UCSC...
GRangesInPromoters-methodsBased on a GRanges and a TxDb, subsets the GRanges to those...
GRannotate-methodsBased on a GRanges and a TxDb, returns the GRanges with a...
GRannotateSimplea GRanges method to split a GRanges in three GRanges:...
GRbaseCoverage-methodsBased on a GRanges and a BAM file, returns a list of base...
GRcoverage-methodsbased on a GRanges and a BAM file, returns the total coverage...
GRcoverageSummit-methodsBased on a GRanges and a BAM file, returns a GRanges with the...
GRenrichment-methodsDetermines the enrichment over a set of genomic regions given...
GRmidpoint-methodsReturns a GRanges containing the mid point of a GRanges
GRsetwidthSet the width of a GRanges based on the mid point of each...
heatmapDataBased on a list of GRanges, determine various kind of counts...
heatmapPlotdisplays the heatmap based on the data from heatmapData
makeGtfFromDbUtilities to transform a TxDb into a GTF file
matchEnhancersGRanges method to match enhancers with putative targets sites
overlapOfGRanges-methodsvisualization of GRanges overlap
palette2dbuild a two dimensional color palette
plotStallingIndexStalling Index plots
simplifyGOtermssimplify a list of GO terms
stallingIndexreturns a list with average read count on TSS, gene body, and...
topGOresdetermines GeneOntology (GO) enriched terms for a set of...
TSSbased on a TxDb returns a GRanges with the TSS positions for...
ucsc2GRangesConvert UCSC-formatted genomic positions into a GRanges
unionMaxScore-methodsGRanges method to perform union of peaks keeping the score of...
Bioconductor-mirror/compEpiTools documentation built on June 1, 2017, 6:39 a.m.