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Getting Started

Installation

Install from PyPI:

pip install leafcutter

Or install from source for development:

git clone https://github.com/leafcutter2/leafcutter-ds.git
cd leafcutter-ds
pip install -e .

Dependencies

Key dependencies installed automatically through pip:

  • numpy, pandas, scipy — core data manipulation
  • pyro-ppl / torch — Bayesian inference backend (for leafcutter-bayes)

CLI Tools

leafcutter-cluster

Clusters introns from RNA-seq junction files.

leafcutter-cluster --help

leafcutter-ds

Runs differential splicing analysis between two groups.

leafcutter-ds --help

leafcutter-bayes

Bayesian differential splicing using Pyro.

leafcutter-bayes --help

leafcutter-gtf-to-exons

A utility tool to make the exons file used in leafcutter-ds from a gtf file.

leafcutter-gtf-to-exons --help

leafcutter-prepare-phenotype

A tool to prepare a splicing phenotype table for downstream sQTL calling tools.

leafcutter-prepare-phenotype --help