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Cuffdiff | Differential analysis of gene regulation at transcript resolution with RNA-seq

Estimates expression at transcript level resolution and controls for variability evident across replicate libraries. Cuffdiff is an algorithm that detects differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes. It can identify genes that display altered inclusion of key features, such as DNA binding regions, in their protein products. Moreover, this software is able to generate accurate transcript-resolution estimates of changes in gene expression.

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Cuffdiff classification

Cuffdiff specifications

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Programming languages:
C, C++

Cuffdiff distribution


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Cuffdiff support


  • Lior Pachter <>
  • John Rinn <>

Additional information


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Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular & Cell Biology, University of California Berkeley, CA, USA

Funding source(s)

Supported by US National Institutes of Health grants DP2OD006670, P01GM099117, P50HG006193, RO1ES020260, R01 HG006129 and R01 DK094699.

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