scSidekick
Reproducible, interpretable single-cell & spatial transcriptomics analysis in R
scSidekick is an open-source R package that takes users from raw count matrices through quality control, integration, clustering, cell-type assignment, differential expression, pathway analysis, and cell–cell communication — while enforcing documentation at every step and producing publication-ready figures, methods text, legends, and PowerPoint exports.
It implements multi-group comparisons, CellChat, inferCNV, cNMF, pseudotime, pseudobulk analysis, ssGSEA, and survival-linked clinical correlation workflows.
- Code: github.com/nourabdelfattah/scSidekick
- Docs: nourabdelfattah.github.io/scSidekick
- Archive: Zenodo 10.5281/zenodo.21285418
- License: MIT
- Status: application note submitted to Bioinformatics