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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




No version available



  • person_outline Yang Li
  • person_outline David Knowles

Additional information


Publication for LeafCutter

LeafCutter citations


Bayesian nonparametric discovery of isoforms and individual specific quantification

Nat Commun
PMCID: 5923247
PMID: 29703885
DOI: 10.1038/s41467-018-03402-w
call_split See protocol

[…] further characterize the functional relationships among these cis-trQTLs, we performed variant set enrichment (VSE) analysis for regions associated with variable intron splicing events identified by LeafCutter, which identifies regions that associate spatially with splicing QTLs and cis-regulatory elements (CREs) from ENCODE in a diverse set of cell types–. VSE is a statistical test that computes […]


Innate Immune Response and Off Target Mis splicing Are Common Morpholino Induced Side Effects in Xenopus

Dev Cell
PMCID: 5861998
PMID: 29478923
DOI: 10.1016/j.devcel.2018.01.022

[…] Splicing anomalies were detected without transcript annotation applying LeafCutter v1.0 () on STAR-aligned split reads from all conditions. LeafCutter focuses on intron splicing events rather than whole transcript isoform quantification which helped to reduce false positi […]


ICE1 promotes the link between splicing and nonsense mediated mRNA decay

PMCID: 5896957
PMID: 29528287
DOI: 10.7554/eLife.33178.037
call_split See protocol

[…] rs (). Reads mapping to constitutive exons and introns of Ensembl GRCh37.87 annotations were quantified with HTSeq (), and a read cutoff stringency of 0.99 was used for REMBRANDTS analysis. Majiq and Leafcutter were used to analyze splicing changes following siICE1 and siNT treatment (; ). For Majiq, a change in isoform usage of 10% or greater at the 95% confidence level was used to identify genes […]


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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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