uabbds/scnanoseq_analysis repository overview

⁠nf-core/scnanoseq

nf-core/scnanoseq is available at https://github.com/nf-core/scnanoseq⁠ and its documentation can be found at: https://nf-co.re/scnanoseq/⁠

For general questions and discussion, please visit the pipeline's nf-core Slack channel⁠.

⁠Docker image for nf-core/scnanoseq validation analysis

The validation analysis of nf-core/scnanoseq (v1.1.0) was performed across datasets derived from 3 sources as detailed in the analysis GitHub: https://github.com/U-BDS/scnanoseq_analysis/tree/main⁠

The scope of the validation focused on performing a subset of tertiary analyses - including QC, filtering, normalization, integration (when applicable), clustering, barcode comparison, cell type identification, and marker evaluation at both the gene and transcript levels-on the outputs of nf-core/scnanoseq to assess its performance against ground-truth data. This analysis does not include other routine scRNA-seq analyses that extend beyond the scope of validation, such as pseudobulk differential gene expression analysis. Additionally, other analytical approaches such as doublet identification was excluded to minimize downstream transformations of the raw data generated by nf-core/scnanoseq. However, we recommend that users should incorporate these common analytical approaches in their own downstream workflows.