scRNAseq Single Sample Processing Cell Ranger
main @ abc9384

Workflow Type: Galaxy
Stable

From 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


Frozen main abc9384
help Creators and Submitter
Creators
  • Sarah Williams
  • Mike Thang
  • Valentine Murigneaux
Submitter
Citation
Williams, S., Thang, M., & Murigneaux, V. (2023). {scRNAseq on galaxy workflows}.
License
Other (Not Open)
Activity

Views: 3307   Downloads: 185   Runs: 2

Created: 9th Nov 2023 at 01:30

Last updated: 30th May 2024 at 06:56

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Total size: 3.6 MB
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