Fetching contributors…
Cannot retrieve contributors at this time
32 lines (20 sloc) 989 Bytes


Velocyto consists of two main components:

  • A command line interface (CLI), that is used to run the pipeline that generates spliced/unspliced expression matrices.
  • A library including functions to estimate RNA velocity from the above mentioned data matrices.

Getting Started

First make sure that velocyto is correctly installed following :ref:`this guide <install>`.

Running the CLI

This guide explains how to run the counting pipeline. It starts from .bam/.sam files to yield a .loom file with counts divided in spliced/unspliced/ambiguous.

.. toctree::

Estimating RNA velocity

This guide covers the analysis and assumes that you have produced a .loom file using the velocyto CLI (follow the guide above).

.. toctree::