BMBL Analysis Notebooks

Internal protocol atlas

BMBL Analysis Notebooks

This site turns the repository into a browsable static reference for BMBL bioinformatics workflows. It is built for readers who already know the assays and analysis ecosystem and need a quicker way to orient themselves to workflow usage, code patterns, committed figures, and source materials.

The repository is not an introduction to sequencing analysis, so this site focuses on workflow usage, expected inputs and outputs, committed figures, and source links rather than runnable notebooks or beginner lessons.

The workflow catalog below is now internalized into the site: each entry is presented as a Quarto page built from committed repository materials without re-executing the notebooks.

Start here

RNA-seq Workflow

Use the featured RNA-seq workflow page as a clear example of the current in-site workflow format: prerequisites, structured steps, committed images, and links back to the source materials.

Use this site for

  • Browse workflows by assay category using the catalog and left-hand navigation
  • Review workflow pages as Tier B usage-and-rationale references
  • Follow GitHub source links when you need the original workflow folders, notebooks, or companion files
  • Use How to Add a Workflow when extending the site

Workflow catalog

Jump to assay family

Browse by assay family. The catalog is intentionally dense and optimized for scanning.

Single-cell RNA-seq

14 workflows

Single-cell ATAC-seq

6 workflows

Single-cell Multi-omics

1 workflow

Single-cell TCR-seq

1 workflow

Spatial Transcriptomics

5 workflows

Bulk RNA-seq / ATAC-seq / ChIP-seq

7 workflows

Bisulfite sequencing

1 workflow

Whole Genome Sequencing

1 workflow

Gene Regulatory Networks

1 workflow

Enrichment / downstream analysis

1 workflow

Data utilities

4 workflows