https://github.com/wtsi-hgi/nf_scrna_qc
Single cell RNA-seq quality control, transcription profile clustering & cell-type assignment
https://github.com/wtsi-hgi/nf_scrna_qc
Last synced: 22 days ago
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Single cell RNA-seq quality control, transcription profile clustering & cell-type assignment
- Host: GitHub
- URL: https://github.com/wtsi-hgi/nf_scrna_qc
- Owner: wtsi-hgi
- License: gpl-3.0
- Created: 2021-12-01T13:49:55.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-03-01T16:25:52.000Z (about 2 years ago)
- Last Synced: 2025-04-15T05:16:36.467Z (22 days ago)
- Language: Python
- Size: 194 KB
- Stars: 4
- Watchers: 3
- Forks: 2
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Description
This pipeline performs data QC and transcription profile clustering for droplet single cell RNA-seq. It starts from gene transcript UMI (unique molecular identfier) counts per barcoded cell. Cell-type assignments for PBMC (peripheral blood mononuclear cells) are also generated.
- [running tests](docs/README-tests.md): run pipeline locally on a small test dataset
- [potential problems and workarounds](docs/README-workarounds.md)
- [input files](docs/README-inputfiles.md)
- [output directory structure](docs/README-outputfiles.md)
# Credits
We thank the following people for their contributions to the development of this pipeline:
Leland Taylor, Matiss Ozols, Guillaume Noell, Hannes Ponstingl, Vivek Iyer, Monika Krzak, Henry Taylor, Tobi Alegbe, Moritz Przybilla