Contact: Cole Trapnell <cole@cs.umd.edu>
Homepage: http://cufflinks.cbcb.umd.edu/
Name: Cufflinks
Reference:
- Author: Cole Trapnell and Brian A Williams and Geo Pertea and Ali Mortazavi and Gordon Kwan and Marijke J van Baren and Steven L Salzberg and Barbara J Wold and Lior Pachter
  Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
  Journal: Nature Biotechnology
  DOI: doi:10.1038/nbt.1621
  URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
  Year: 2010
  PMID: 20436464
  Pages: 511-515
  Volume: 28
  Number: 5
  Type: article
- Author: "Cole Trapnell and Adam Roberts and Loyal Goff and Geo Pertea and Daehwan Kim and David R Kelley and Harold Pimentel and Steven L Salzberg and John L Rinn and Lior Pachter"
  Title: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
  Journal: Nat. Protocols
  Year: 2012
  DOI: 10.1038/nprot.2012.016
  URL: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
  Pages: 562-578
  Volume: 7
  Number: 8
  PMID: 22383036
  Type: article
