LeafCutter protocols

View LeafCutter computational protocol

LeafCutter statistics

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chevron_left Alternative splicing events identification Differential usage Splicing QTL detection Novel transcript quantification chevron_right
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Associated diseases

Associated diseases

LeafCutter specifications


Unique identifier OMICS_11334
Name LeafCutter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Apache License version 2.0
Computer skills Advanced
Version 0.2.7
Stability Stable
rstan, foreach, ggplot2, R.utils, gridExtra, reshape2, Hmisc
Maintained Yes



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  • person_outline Yang Li <>
  • person_outline David Knowles <>

Additional information


Publication for LeafCutter

LeafCutter in pipeline

PMCID: 5499207
PMID: 28604674
DOI: 10.1038/ncomms15824

[…] by the s.d. of the normalized expression level of the respective gene. the p values corresponding to the were corrected for multiple testing using the hochberg family-wise error rate method., the leafcutter software was utilized to detect aberrant splicing. each patient was tested against all others. to adjust leafcutter to the rare disease setting, we modified the parameters to detect rare […]

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LeafCutter institution(s)
Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Radiology, Stanford University, Stanford, CA, USA; UCL Genetics Institute, London, UK; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA; Department of Biology, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
LeafCutter funding source(s)
Supported by a CEHG fellowship, the Howard Hughes Medical Institute, and the US National Institutes of Health (NIH grants HG007036, HG008140, and HG009431 and MH107666).

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