Useful code

A collection of bioinformatics guides and project examples in R, Python, and Quarto. Guides provide compact starting points; examples retain project context.

Caution

These workflows are not validated for your study. Review their inputs, assumptions, software versions, and outputs before reuse. They are not for clinical or diagnostic decisions.

Methods catalog · Templates · Examples · Other resources

The catalog previews each Quarto guide on site and lists its inputs, analysis unit, outputs, key limit, and verification status.

Methods

Area	Guides	Focus
Single-cell	3	Seurat, AnnData velocity and activity, pyUCell signatures
Bulk RNA	1	tximport, edgeR, enrichment, and sample scoring
scATAC	1	Signac QC, peak testing, motifs, and chromVAR
Multiome	1	Paired RNA/ATAC QC, WNN, linkage, and label transfer
MOFA2	1	Matched views, factors, and diagnostics
Biomarker ML	1	Patient-grouped held-out evaluation

The template guide lists all eight workflows. The examples preserve project-specific context and methods.

Reuse a workflow

1. Confirm that the input, identifiers, and study design match the guide.
2. Check package versions and current upstream documentation.
3. Set paths and scientific choices for your data.
4. Review diagnostics and validate outputs before interpretation.

Guide status: draft means the workflow has not been checked on representative data. It does not certify or invalidate a scientific method.

Repository map

Path	Contents
templates/	Reusable analysis guides
examples/	Project-specific workflows and provenance
functions/	Small shared R and Python helpers
miscellaneous/	Reporting and documentation resources
scripts/	Repository checks
website/	Searchable catalog and downloads
archive/	Superseded material and historical records

GitHub Actions checks document structure, paths, and syntax. It does not run the bioinformatics analyses.

File conventions

• Seurat objects: .qs2
• AnnData objects: .h5ad
• Tables: TSV
• MOFA2 models: native HDF5

License

Released under the MIT License.