scRNAseq Single Sample Processing Cell Ranger main @ abc9384
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Run on GalaxyFrom the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData Depreciated: use individual workflows insead for multiple samples
Steps
| ID | Name | Description |
|---|---|---|
| 7 | scRNAseq: Count and Load with Cell Ranger | n/a |
| 8 | scRNAseq_CellQC | n/a |
| 9 | scRNAseq_QCtoBasicProcessing | n/a |
Version History
main @ abc9384 (earliest) Created 9th Nov 2023 at 01:30 by Sarah Williams
now with cellranger pipelines
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Created: 9th Nov 2023 at 01:30
Last updated: 30th May 2024 at 06:56
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Teams: QCIF Bioinformatics
Organizations: QCIF
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia, National Computational Infrastructure (NCI) WorkflowHub team
Web page: https://www.biocommons.org.au/
Working closely with researchers, the QCIF Bioinformatics team apply data management, processing, integration, analysis and visualisation techniques to maximise the potential value of biological and clinical data sets. QCIF Bioinformatics is a partner in the Australian BioCommons.
Space: Australian BioCommons
Public web page: https://www.qcif.edu.au/
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 ...
