[Blends-commit] r2638 - in /projects/med/trunk/debian-med/tasks: bio bio-ngs

[plessy at users.alioth.debian.org]

Author: plessy
Date: Sun Jan 30 01:54:04 2011
New Revision: 2638

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2638
Log:
Added cufflinks, see <http://git.debian.org/?p=debian-med/cufflinks.git>.

Modified:
    projects/med/trunk/debian-med/tasks/bio
    projects/med/trunk/debian-med/tasks/bio-ngs

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2638&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sun Jan 30 01:54:04 2011
@@ -3167,6 +3167,24 @@
 Published-URL: http://genomebiology.com/2009/10/11/R134
 Published-DOI: 10.1186/gb-2009-10-11-r134
 
+Depends: cufflinks
+Homepage: http://cufflinks.cbcb.umd.edu/
+Vcs-Git: http://git.debian.org/?p=debian-med/cufflinks.git
+License: Boost
+X-Category: Sequencing
+Pkg-Description: Transcript assembly, differential expression, and differential 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. 
+Published-Authors: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
+Published-Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
+Published-In: Nature Biotechnology
+Published-DOI: doi:10.1038/nbt.1621
+Published-URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
+Published-Year: 2010
+
 Depends: ncbi-tools++
 Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
 License: Public domain except for some third-party LGPLed code

Modified: projects/med/trunk/debian-med/tasks/bio-ngs
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-ngs?rev=2638&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Sun Jan 30 01:54:04 2011
@@ -25,6 +25,17 @@
  reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep
  its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB
  for paired-end).
+
+Depends: cufflinks
+Homepage: http://cufflinks.cbcb.umd.edu/
+Vcs-Git: http://git.debian.org/?p=debian-med/cufflinks.git
+License: Boost
+Pkg-Description: Transcript assembly, differential expression, and differential 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. 
 
 Depends: mira
 Homepage: http://chevreux.org/projects_mira.html