Man pages for compEpiTools
Tools for computational epigenomics
| compEpiTools-package | Tools for computational epigenomics |
| countOverlapsInBins-methods | given a query and a subject GRanges returns a matrix of... |
| distanceFromTSS-methods | Returns the GRanges annotated with info about the closer TSS |
| enhancers | A GRanges method to define enhancers based on H3K4me1 peaks |
| findLncRNA | Identify putative long non coding RNAs (lncRNA) |
| getPromoterClass-methods | Determining the CpG promoter class and the average CpG... |
| GR2fasta-methods | A GRanges method to extract and write to the disk a fasta... |
| GRanges2ucsc-methods | A GRanges method to convert ranges information into UCSC... |
| GRangesInPromoters-methods | Based on a GRanges and a TxDb, subsets the GRanges to those... |
| GRannotate-methods | Based on a GRanges and a TxDb, returns the GRanges with a... |
| GRannotateSimple | a GRanges method to split a GRanges in three GRanges:... |
| GRbaseCoverage-methods | Based on a GRanges and a BAM file, returns a list of base... |
| GRcoverage-methods | based on a GRanges and a BAM file, returns the total coverage... |
| GRcoverageSummit-methods | Based on a GRanges and a BAM file, returns a GRanges with the... |
| GRenrichment-methods | Determines the enrichment over a set of genomic regions given... |
| GRmidpoint-methods | Returns a GRanges containing the mid point of a GRanges |
| GRsetwidth | Set the width of a GRanges based on the mid point of each... |
| heatmapData | Based on a list of GRanges, determine various kind of counts... |
| heatmapPlot | displays the heatmap based on the data from heatmapData |
| makeGtfFromDb | Utilities to transform a TxDb into a GTF file |
| matchEnhancers | GRanges method to match enhancers with putative targets sites |
| overlapOfGRanges-methods | visualization of GRanges overlap |
| palette2d | build a two dimensional color palette |
| plotStallingIndex | Stalling Index plots |
| simplifyGOterms | simplify a list of GO terms |
| stallingIndex | returns a list with average read count on TSS, gene body, and... |
| topGOres | determines GeneOntology (GO) enriched terms for a set of... |
| TSS | based on a TxDb returns a GRanges with the TSS positions for... |
| ucsc2GRanges | Convert UCSC-formatted genomic positions into a GRanges |
| unionMaxScore-methods | GRanges method to perform union of peaks keeping the score of... |
