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 |