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urmi-21 committed Jan 16, 2021
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Tutorial
========

This tutorial provides introduction to pyrpipe.
New users can start here to get an idea how to use pyrpipe APIs for RNA-Seq or other analysis.
This tutorial provides an introduction to pyrpipe.
New users can start here to get an idea of how to use pyrpipe APIs for RNA-Seq or other analysis.
This tutorial is divided into smaller sections.

First section describes the recommended way of installing pyrpipe and setting up conda environments.
Section 1 describes the recommended way of installing pyrpipe and setting up conda environments.

Then, an introduction to basic RNA-Seq API is provided via a simple RNA-Seq processing pipeline example.
Section 2 is an introduction to basic RNA-Seq API is provided via a simple RNA-Seq processing pipeline example.

After that, there is information on how to extend pipelines using third-party tools and integrate pyrpipe into snakemake for more scalable workflows.
Section 3 provides information on how to extend pipelines using third-party tools and integrate pyrpipe into snakemake for more scalable workflows.

The latter topics provide cover details on pyepipe_engine, pyepipe_module and pyrpipe_diagnostic which provide many useful and helpful functionality.
Subsequent Sections detail pyrpipe_engine, pyrpipe_module and pyrpipe_diagnostic, each of which provide reproducibility and helpful functionality.


.. toctree::
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