This project aims to enhance the nf-core/scdownstream pipeline for downstream scRNA-seq analysis. By expanding the range of available tools, we will improve its functionality, fostering broader adoption and making the pipeline more up-to-date and appealing to the scientific community.
Goals
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Expanding the range of doublet detection tools to include better-performing tools, particularly scDblFinder.
- For people who have experience with scRNA-seq QC in Python or R
- Based on benchmark comparisons, scDblFinder generally outperforms the currently listed tools.
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Expanding the range of cell type annotation tools to include other species currently not accounted for, particularly mice.
- For people who have experience with mouse or other model organism’s scRNA-seq data analysis
- Datasets like Tabula Muris (Senis) will be explored for support integration.
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Improving documentation and user support to promote broader adoption.
- For first-time contributors interested in making the pipeline more accessible!
Contributors of all experience levels are welcome!
category
pipelines
