academic/cufflinks: Added (reference-guided assembler for RNA-Seq).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 37 insertions, 0 deletions

diff --git a/academic/cufflinks/References b/academic/cufflinks/References
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+Publications
+
+Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ,
+Salzberg SL, Wold B, Pachter L. Transcript assembly and quantification
+by RNA-Seq reveals unannotated transcripts and isoform switching
+during cell differentiation
+Nature Biotechnology doi:10.1038/nbt.1621
+
+Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-
+Seq expression estimates by correcting for fragment bias
+Genome Biology doi:10.1186/gb-2011-12-3-r22
+
+Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel
+transcripts in annotated genomes using RNA-Seq
+Bioinformatics doi:10.1093/bioinformatics/btr355
+
+Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L
+Differential analysis of gene regulation at transcript resolution with
+RNA-seq
+Nature Biotechnology doi:10.1038/nbt.2450
+
+REFERENCES
+---------------------------
+Cufflinks builds on many ideas, including some
+proposed in the following papers:
+
+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)
+
+Hui Jiang and Wing Hung Wong, "Statistical Inferences for isoform expression", 
+Bioinformatics, 2009 25(8):1026-1032
+
+Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, 
+Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel, "Viral 
+population estimation using pyrosequencing", PLoS Computational Biology, 
+4(5):e1000074