Dear developers,
The package casper is now available in the Bioc devel branch. casper
implements novel methodology to infer alternative splicing from paired-end
RNA-seq data, which we have found may cut the estimation Mean Square Error
by up to a factor of 4.
Its basic features:
- Summarizes reads in a novel, more informative way. Instead of simply
considering counts for exons / exon junctions, casper considers full exon
paths. This avoids throwing away information for up to 2/3 of the reads.
- Estimates non-parametrically the distribution of reads across the
transcript (i.e. in particular, it does NOT assume read uniformity). Also,
estimates non-parametrically the insert size distribution
- By default, obtains expression estimates that are regularized to be away
from 0. This can be interpreted either as a posterior mode under a mildly
informative prior, or as a penalized likelihood approach.
- Provides functions to process bam files, download available genome
annotations, return results in ExpressionSets. It also has some plotting
capabilities.
- Currently it deals with known variants. We are currently implementing a
de novo search.
Additional to advertising the package, I have one question for the list
(sorry, kind of basic but I couldn't find the answer, plus the fhcrc wiki
seems to be down). Does anybody know how can I add additional developers to
the svn repository?
Thanks,
David
David Rossell, PhD
Manager, Biostatistics & Bioinformatics Unit
IRB Barcelona (Spain)
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