Spec URL: http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks.spec SRPM URL: http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks-0.9.3-1.fc15.src.rpm Description: 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. Cufflinks is a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg's group at the University of Maryland Center for Bioinformatics and Computational Biology, and Barbara Wold's lab at Caltech.
New version with various fixes and latest upstream release: http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks.spec http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks-1.0.1-1.fc16.src.rpm
New upstream release: http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks.spec http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks-1.0.3-1.fc16.src.rpm
That package seems to include lemon and locfit. I just took a quick look though. There's also a binary in the tarball: cuffmerge. Better delete that!
Update to latest upstream at: http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks.spec http://verdurin.fedorapeople.org/reviews/cufflinks/cufflinks-1.3.0-1.fc16.src.rpm 'cuffmerge' is a Python script. I've made a start on 'lemon' and 'locfit', for which I'll submit separate review requests.
How's it going here?
I see version 2 has been released since I last looked at this. Will get back into it.
I'm no longer working in this field, so if anyone wants to take up this review request, feel free.
I could take this on, but I'm not sure the licence of the locfit component is free; see the usage exception in the extract below. (This is missing from the cufflinks distribution, though I sent a copy of the README to the maintainer, obtained from the tarball under http://cm.bell-labs.com/stat/project/locfit/.) The version in the R CRAN repository doesn't have this clause, but is missing files that appear to be needed for cufflinks. lemon has just been packaged. ABOUT ALGORITHMS: The Locfit implementation has been designed largely from the point of view of generality: to provide a set of functions that can be used for as wide a range of local fitting problems as possible. It is not intended to be the fastest or most efficient implementation possible. In addition to generality, the code in many places makes extensive trade-offs made between speed and numerical accuracy (some of which can be controlled through optional arguments). Many of Locfit's options will only be used in a small fraction of cases; for other cases, they add to the cost of overhead (an obvious example is multi-dimensional fitting: when used in 1-d, many loops reduce to for(i=0;i<1;i++)). Additionally, the user interfaces (i.e. the R and S-Plus code) add significantly to the computational overhead. For these reasons, the Locfit code, as distributed, should not, and can not, be used to derive meaningful benchmarks, either for the speed or accuracy of algorithms. Anyone wishing to use Locfit in any kind of comparative benchmark study must contact and obtain permission from the Author. COPYRIGHT: Copyright (c) 1996-2001 Lucent Technologies, Bell Laboratories. SCB code is Copyright (c) 1996-2001 Jiayang Sun. Permission to use, copy, modify, and distribute this software for any purpose (with the exceptions noted in `About Algorithms' above) without fee is hereby granted, and provided that this entire notice is included in all copies of any software which is or includes a copy or modification of this software and in all copies of the supporting documentation for such software. THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. IN PARTICULAR, NEITHER THE AUTHOR NOR LUCENT TECHNOLOGIES MAKE ANY REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE.
Yes, the license of locfit was one of the things that put me off.