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Guide scRNAseq Processing Workflow landing page

About

This document describes how to use some scanpy-based scRNAseq workflows on galaxy Australia.

The aim of these workflows is to handle the routine ‘boring’ part of single cell RNAseq data processing. It will produces an ‘AnnData’ object, which can then be used as a base for downstream analysis – either within galaxy or outside of it. AnnData is a standard format used by the ‘scanpy’ python package.

These workflows represent just one way of processing data for a ‘typical’ scRNAseq experiment – there are many other options!

The how-to guide is available here

Contributors

MT
Author

Mike Thang

QCIF Bioinformatics / University of Queensland

SW
Author

Sarah Williams

QCIF Bioinformatics / Griffith University

VM
Author

Valentine Murigneaux

QCIF Bioinformatics / University of Queensland

Please cite this guide as follows

Please ensure you cite all the tools within this workflow that you use in your work (see references section), and consider also citing the Clustering 3kPBMCs with Scanpy tutorial tutorial upon which these workflows are based.

Acknowledgements

The workflows are based on the excellent Clustering 3kPBMCs with Scanpy tutorial

This guide makes use of the ELIXIR toolkit theme: theme badge

References

These workflows depend on the following tools and resources;