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Single-cell RNA

3 notebooks

Single-cell analysis with Seurat, AnnData, and pyUCell.

Includes: Seurat QC and inference; AnnData velocity and activity; Python signature scoring

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Bulk RNA

1 notebooks

One count-aware edgeR workflow from tximport through sample-level scoring.

Includes: tximport, QC, differential expression, GSEA, singscore, GSVA

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scATAC-seq

1 notebooks

One Signac workflow from count matrix and fragments through motif analysis.

Includes: Signac QC, LSI, differential peaks, motifs, chromVAR

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Multiome

1 notebooks

One paired RNA/ATAC workflow for QC, WNN, linkage, and label transfer.

Includes: paired QC, weighted nearest neighbors, peak-gene links, label transfer

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Multi-omics / MOFA

1 notebooks

One MOFA2 workflow from matched views through model diagnostics and interpretation.

Includes: view matching, fitting, factors, variance, weights

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Biomarker machine learning

1 notebooks

One sample-level bias-reduced classifier with a locked held-out evaluation.

Includes: brglm2 classification and held-out reporting

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