Transcript assembly, differential expression and regulation for RNA-Seq

 Cufflinks assembles transcripts, estimates their abundances, and
 tests for differential expression and regulation in RNA-Seq samples.
 It accepts aligned RNA-Seq reads and assembles the alignments into a
 parsimonious set of transcripts. Cufflinks then estimates the
 relative abundances of these transcripts based on how many reads
 support each one.
 .
 This package provides the binary of cufflinks and associated tools, i.e.
 compress_gtf, cuffcompare, cuffdiff, cuffmerge, cuffnorm, cuffquant and
 gtf_to_sam.