README

We start it as a package just to easy install to R.

0.0.1 - initial version, nothing works yet
0.0.2 - we can: 
	prepare uniform intervals (noodles)
	calcutate the coverage for intervals & list of bed files
	generate a list of genes that are around (+-flanks) ranges from GRanges
0.0.3 - tabulated fisher added
0.0.4 - annotaion functions improved; roxygen documentation added
0.0.5 - annotation function fixed; names changed
0.0.6 - working annotation functions : 
	genes.with.TSS.covered.by.interval, genes.with.TSS.covered, closest.gene.start.by.interval
0.0.7 - CountCoverageOfNoodles returns sparse Matrix
0.0.8 - count.coverage.of.noodles is a new version; now, it correctly works with bed intervals that are longer than noodles; max(coverage of noodle)==width(noodle). indicate.any.coverage.of.noodles added. 
0.0.9 - added support for hg18
0.1.0 - function max.peak.score.for.each.noodle added
0.1.1 - added support for hg38
0.1.2 - closest.gene.start.by.interval fixed. Now, it works even if a moodle is located on an chromosome that has no known genes.
0.1.3 - genes.intersected function added
0.1.4 - single.strand.genes.only=FALSE in gene() call adds ~4000 more genes
0.1.5 - closest.gene.start.by.interval modified closest.gene.by.interval added
0.1.6 - documentation is more roxygenned
0.1.7 - works with seqlengths from the genome rather that requires the noodles to have correct seqinfo/seqlengths
0.1.8 - works with gencode and ucsc genome annotations
0.1.9 - adds ensemble or gene_id to the output gene list
0.2.0 - added mouse genome; moved all the known gene tables to /data
0.2.1 - added gencode hs28
0.2.2 - fixed an strange behaviour when noodles and lengehes parameters both provided seqlengths, thanks to Vera Mukhina from UMD