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rDiff | Detection of differential RNA processing

Detects differential abundances of RNA isoforms in pairs of biological samples. rDiff is composed of two approaches: (i) rDiff.parametric supplies a method that can be used to identifying regions with alternative isoform expression; and (ii) rDiff.nonparametric, based on permutations, that does not depend of the underlying isoform structure and is especially suited for newly sequenced genomes only determined by homology.

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rDiff classification

rDiff specifications

Unique identifier:
Command line interface
Input format:
Biological technology:
Illumina, Pacific Biosciences
GNU General Public License version 3.0
Software type:
Restrictions to use:
Output format:
Operating system:
Unix/Linux, Mac OS
Computer skills:
Octave or Matlab, Scipy, Samtools, wget

rDiff distribution


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rDiff support


  • Gunnar Rätsch <>
  • Gunnar Rätsch <>
  • Philipp Drewe <>


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Computational Biology Center, Sloan-Kettering Institute, New York, NY, USA; Friedrich Miescher Laboratory of the Max-Planck Society, Tubingen, Germany; Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems, Tubingen, Germany; Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany; Center for Plant Mol. Biology, University of Tubingen, Tubingen, Germany; Center for Bioinformatics, University of Tubingen, Tubingen, Germany

Funding source(s)

Supported by Volkswagen foundation and Marie Curie FP7 fellowship; German Research Foundation [WA2167/4-1; RA1894/1-1 and RA1894/2-1]; Emmy Noether fellowship [WA2167/2-1]. MSKCC Center for Translational Cancer Genomic Analysis [U24 CA143840]; and Sloan-Kettering Institute core funding.

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