Browse the notebooks by analysis type. Each entry has a short description and links to view or download the QMD file.

Single-cell

16 notebooks

Seurat and Python notebooks for building objects, QC, normalization, scoring, markers, trajectories, dynamics, and network analysis.

Includes: Seurat QC, Harmony, UCell, and trajectory analysis

Browse family →

Bulk RNA

6 notebooks

Count-aware edgeR import and QC, differential-expression reminders, ranked enrichment, and sample-level gene-set scores.

Includes: tximport/edgeR, GSEA, singscore, and GSVA

Browse family →

scATAC

5 notebooks

Signac notebooks for object construction, fragment-aware QC, TF-IDF/LSI, motif enrichment, and a chromVAR API reminder.

Includes: Signac QC, LSI, motif enrichment, and chromVAR

Browse family →

Multiome

4 notebooks

Paired RNA/ATAC notebooks for object construction, weighted nearest neighbors, peak–gene linkage, and label transfer.

Includes: WNN, peak–gene linkage, and RNA-to-ATAC label transfer

Browse family →

Multi-omics / MOFA

4 notebooks

MOFA2 notebooks for view preparation, model fitting, diagnostics, and interpretation across named multi-omics views.

Includes: view preparation, fitting, diagnostics, and interpretation

Browse family →

Biomarker machine learning

2 notebooks

Small-cohort biomarker classification and frozen model reporting with held-out evaluation.

Includes: brglm2 classification and frozen model reporting

Browse family →