GRangesInPromoters-methods
Based on a GRanges and a TxDb, subsets the GRanges to those
regions overalpping with promoters
Tools for computational epigenomics
countOverlapsInBins-methods
given a query and a subject GRanges returns
a matrix of counts of subject in bins of query
displays the heatmap based on the data from heatmapData
Utilities to transform a TxDb into a GTF file
Based on a GRanges and a TxDb, returns the GRanges with a series
of annotations
build a two dimensional color palette
Stalling Index plots
Returns the GRanges annotated with info about the closer TSS
A GRanges method to convert ranges information into UCSC format
A GRanges method to extract and write to the disk a fasta file
containing genomic sequences for the GRanges regions in a genome
Based on a list of GRanges, determine various kind of counts
before displaying a heatmap
Set the width of a GRanges based on the mid point of each region
GRanges method to match enhancers with putative targets sites
visualization of GRanges overlap
A GRanges method to define enhancers based on H3K4me1 peaks
Determines the enrichment over a set of genomic regions given two
BAM files
Returns a GRanges containing the mid point of a GRanges
Convert UCSC-formatted genomic positions into a GRanges
GRanges method to perform union of peaks keeping the score of the
most significant peak
based on a GRanges and a BAM file, returns the total coverage for
each range, or for each bin of the range.
Based on a GRanges and a BAM file, returns a GRanges with the
positions of maximum coverage within each range
determines GeneOntology (GO) enriched terms for a set of Entrez
gene ids
based on a TxDb returns a GRanges with the TSS positions for all
transcripts
Identify putative long non coding RNAs (lncRNA)
a GRanges method to split a GRanges in three GRanges: promoter,
intragenic and intergenic
Based on a GRanges and a BAM file, returns a list of base
coverage vectors for each range
simplify a list of GO terms
returns a list with average read count on TSS, gene body, and
stalling index for a number of samples
Determining the CpG promoter class and the average CpG content