SlackBuilds Repository

14.1 > Academic > cufflinks (2.2.1)

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, taking into account biases in library preparation protocols.

Cufflinks is a collaborative effort between the Laboratory for
Mathematical and Computational Biology, led by Lior Pachter at UC
Berkeley, Steven Salzberg's computational genomics group at the
Institute of Genetic Medicine at Johns Hopkins University, and Barbara
Wold's lab at Caltech.

Reference:
Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and
Barbara Wold, "Mapping and quantifying mammalian transcriptomes by
RNA-Seq", Nature Methods, volume 5, 621 - 628 (2008)

This requires: eigen3, samtools

Maintained by: Petar Petrov
Keywords: bioinformatics,sequence,RNA-Seq,transcript

Homepage:
http://cufflinks.cbcb.umd.edu/

Source Downloads:
cufflinks-2.2.1.tar.gz (9a5ba7a7710cd864932cf205c17851f0)

Download SlackBuild:
cufflinks.tar.gz
cufflinks.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Individual Files:
README
References
cufflinks.SlackBuild
cufflinks.info
slack-desc

See our HOWTO for instructions on how to use the contents of this repository.

Access to the repository is available via:
ftp git cgit http rsync

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