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See:
Description
Class Summary | |
AnnotateRegions | For annotating Intervals or binding regions with gene information, proximity, neighbors, and bias based on random trials. |
AnnotateRegionsWithGeneList | For annotating a picks file (chr, start, stop) with gene information for a particular list of CG names. |
BindingRegion | For holding information about a genomic interval, what genes are up, down, overlap, or contain this genomic inteval. |
BindingRegionComparator | |
BindingRegionsToGff3 | Converts a Binding GenomicRegion file into GFF3 format. |
BindingRegionsToIntervals | Converts binding regions to intervals setting the binding region as the best window and adds 2kb on either side. |
DmelCGNameCoordinatePrinter | Prints genome coordinates for Dmel Rel 4 GFF3 CG names. |
Gff2ToBindingRegions | Converts a gff2 file to a binding region file (chr start end mockSequence). |
Gff2ToIntervals | Converts a gff2 file to an interval object file. |
IntersectBindingPeaks | Performs an intersection analysis on two peak pick files (chr peakPosition score). |
IntersectKeyWithRegions | Takes a key from a spike in experiment and sorted lists of regions to calculate TPR, FPR, and FDR for every threshold |
IntersectRegions | Performs an intersection analysis on binding region files (chr start stop (optional fraction gc)). |
MergeRegions | Takes several tab delimited region files (chrom, start, stop, ...), creates the union and writes to disk. |
RandomRegions | Use to generate random regions of a defined length from a file of regions (chrom, start, stop). |
Region | Represents a genomic region. |
RegionComparator |
For associating intervals, binding regions, and binding peaks with GFF annotation.
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