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find a way to visualize the diff exp rna seq data #22

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
already created an importer to glob all cuffdiff output into sql lite. I have a 
few queries that directly produce a IGV track that may be interesting.

I need science/stat guy to help validate (vasu?)

Original issue reported on code.google.com by zack...@gmail.com on 7 Apr 2011 at 8:57

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 7 Apr 2011 at 8:57

GoogleCodeExporter commented 8 years ago 
Possible solution: Jonathan has a track viewer for Cufflink (gtf) with 
collapsible viewing of tracks and reads.

Original comment by dmagli...@gmail.com on 7 Apr 2011 at 10:03

GoogleCodeExporter commented 8 years ago 
Zack, I think IGV viewer  should be best. Do You still need to discuss. I 
joined the project late.

Original comment by vasup...@gmail.com on 13 Apr 2011 at 6:27

GoogleCodeExporter commented 8 years ago 
cummeRbund looks interesting

Original comment by zack...@gmail.com on 7 Feb 2012 at 10:50

GoogleCodeExporter commented 8 years ago 
funny you should mention it, that's what I started reprocessing the LAML BAMs 
for.  A paper that is currently under review compares CuffDiff to DEXSeq and 
finds that the former systematically underestimates dispersion, with 
predictable results.

http://precedings.nature.com/documents/6837/version/1

It may be worthwhile to use cummeRbund to compare the two for our purposes. 
DEXSeq has plotting functions to visualize differential exon usage, as does 
cummeRbund.  I am also working on a slightly more simplistic approach using the 
'genoset' package.

Original comment by tim.tri...@gmail.com on 8 Feb 2012 at 4:27

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 7 Aug 2012 at 8:07