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| compEpiTools-package | Tools for computational epigenomics |
| compEpiTools | Tools for computational epigenomics |
| countOverlapsInBins | given a query and a subject GRanges returns a matrix of counts of subject in bins of query |
| countOverlapsInBins-method | given a query and a subject GRanges returns a matrix of counts of subject in bins of query |
| countOverlapsInBins-methods | given a query and a subject GRanges returns a matrix of counts of subject in bins of query |
| distanceFromTSS | Returns the GRanges annotated with info about the closer TSS |
| distanceFromTSS-method | Returns the GRanges annotated with info about the closer TSS |
| distanceFromTSS-methods | Returns the GRanges annotated with info about the closer TSS |
| enhancers | A GRanges method to define enhancers based on H3K4me1 peaks |
| enhancers-method | A GRanges method to define enhancers based on H3K4me1 peaks |
| enhancers-methods | A GRanges method to define enhancers based on H3K4me1 peaks |
| featuresLength | Utilities to transform a TxDb into a GTF file |
| featuresLength-method | Utilities to transform a TxDb into a GTF file |
| featuresLength-methods | Utilities to transform a TxDb into a GTF file |
| findLncRNA | Identify putative long non coding RNAs (lncRNA) |
| getPromoterClass | Determining the CpG promoter class and the average CpG content |
| getPromoterClass-method | Determining the CpG promoter class and the average CpG content |
| getPromoterClass-methods | Determining the CpG promoter class and the average CpG content |
| GR2fasta | A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome |
| GR2fasta-method | A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome |
| 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 |
| GRanges2ucsc | A GRanges method to convert ranges information into UCSC format |
| GRanges2ucsc-method | A GRanges method to convert ranges information into UCSC format |
| GRanges2ucsc-methods | A GRanges method to convert ranges information into UCSC format |
| GRangesInPromoters | Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters |
| GRangesInPromoters-method | Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters |
| GRangesInPromoters-methods | Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters |
| GRannotate | Based on a GRanges and a TxDb, returns the GRanges with a series of annotations |
| GRannotate-method | Based on a GRanges and a TxDb, returns the GRanges with a series of annotations |
| GRannotate-methods | 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 |
| GRannotateSimple-method | a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic |
| GRannotateSimple-methods | a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic |
| GRbaseCoverage | Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range |
| GRbaseCoverage-method | Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range |
| GRbaseCoverage-methods | 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, or for each bin of the range. |
| GRcoverage-method | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range. |
| GRcoverage-methods | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range. |
| GRcoverageInbins | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range. |
| GRcoverageInbins-method | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range. |
| GRcoverageInbins-methods | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range. |
| GRcoverageSummit | Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range |
| GRcoverageSummit-method | Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range |
| GRcoverageSummit-methods | 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 |
| GRenrichment-method | Determines the enrichment over a set of genomic regions given two BAM files |
| GRenrichment-methods | Determines the enrichment over a set of genomic regions given two BAM files |
| GRmidpoint | Returns a GRanges containing the mid point of a GRanges |
| GRmidpoint-method | Returns a GRanges containing the mid point of a GRanges |
| 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 region |
| GRsetwidth-method | Set the width of a GRanges based on the mid point of each region |
| GRsetwidth-methods | Set the width of a GRanges based on the mid point of each region |
| heatmapData | Based on a list of GRanges, determine various kind of counts before displaying a heatmap |
| heatmapPlot | displays the heatmap based on the data from heatmapData |
| makeGtfFromDb | Utilities to transform a TxDb into a GTF file |
| makeGtfFromDb-method | Utilities to transform a TxDb into a GTF file |
| makeGtfFromDb-methods | Utilities to transform a TxDb into a GTF file |
| matchEnhancers | GRanges method to match enhancers with putative targets sites |
| matchEnhancers-method | GRanges method to match enhancers with putative targets sites |
| matchEnhancers-methods | GRanges method to match enhancers with putative targets sites |
| overlapOfGRanges | visualization of GRanges overlap |
| overlapOfGRanges-method | visualization of GRanges overlap |
| 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 stalling index for a number of samples |
| 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 |
| ucsc2GRanges | Convert UCSC-formatted genomic positions into a GRanges |
| unionMaxScore | GRanges method to perform union of peaks keeping the score of the most significant peak |
| unionMaxScore-method | GRanges method to perform union of peaks keeping the score of the most significant peak |
| unionMaxScore-methods | GRanges method to perform union of peaks keeping the score of the most significant peak |