scRNAseq processing in galaxy

This collection houses 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:https://github.com/swbioinf/scrnaseq_howto_ga_workflows

These workflows are based on the 'Clustering 3K PBMCs with Scanpy' tutorial (Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman) https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.html.