cycombinepy

cycombinepy is a Python port of cyCombine for batch correction of single-cell cytometry data. It is AnnData-native and reuses mature Python libraries for the numerical heavy lifting:

Component	Library
ComBat correction	inmoose.pycombat
SOM clustering	FlowSOM
FCS I/O	pytometry
Batch-effect metrics	scib-metrics

The pipeline ported over unchanged from the R package is:

1. Batch-wise normalize each marker (cycombinepy.normalize)

2. Self-organizing map clustering of cells (cycombinepy.create_som)

3. Per-cluster ComBat correction with optional covariates (cycombinepy.correct_data)

Step 1 operates on a normalized view so that downstream clusters represent biology rather than technical variation. Step 3 is applied to the unnormalized data per cluster so rare populations are not over-corrected.

Getting started

• Installation
  • Requirements
  • Install from PyPI
  • Install from source (development)
  • Building the documentation
  • Verifying the installation
• Usage guide
  • Data conventions
  • The pipeline in one call
  • Loading data
  • Preprocessing
  • Normalization
  • Clustering
  • Per-cluster ComBat correction
  • Evaluating a correction
  • Detecting batch effects
  • Plotting helpers

Tutorials

• Main cyCombine workflow (Python port)
  • Setup
  • Download the data
  • Load FCS files into AnnData
  • Prepare data — arcsinh transform
  • Inspect the batch effect
  • Batch correction — recommended one-shot API
  • Batch correction — modular API
  • Evaluate — EMD reduction
  • Visualize — before vs. after correction
  • Persisting results
  • What next?
• Detecting batch effects (Python port)
  • Cofactor guidance
  • Setup
  • Load the Nuñez PBMC dataset
  • detect_batch_effect_express — the quick summary
  • detect_batch_effect — the full diagnostic
  • Interpreting the diagnostics

Reference

• API reference
  • Preprocessing
  • Clustering
  • Correction
  • Evaluation
  • Detection
  • Utilities
  • I/O
  • Plotting
  • Advanced evaluation

Indices

• Index

• Module Index

• Search Page