PERSONAL RESEARCH COOKBOOK

Readable workflows for real analytical work.

A personal collection of R, Python, and Quarto notebooks for common bioinformatics analyses. Browse by topic, then open a notebook on GitHub when you want the code.

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37notebooks

6method areas

Personal research scripts. These are not drop-in pipelines. Check the assumptions and validate them on your own data before reuse. Read the full disclaimer.

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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

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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

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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

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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

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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

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Biomarker machine learning

2 notebooks

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

Includes: brglm2 classification and frozen model reporting

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Other resources

Browse Examples and Miscellaneous for project notebooks and reporting material.