campmc#
campmc is a third-party, Scanpy-style Python package for CAMP metacell partitioning on AnnData objects.
Online documentation: campmc.readthedocs.io
Note
This site documents the campmc package — an independent port for portable use with Scanpy. It is not the official documentation of the CAMP paper authors. For the reference implementation and paper benchmarks, see upstream CAMP.
Quick start#
import campmc as cp
import scanpy as sc
adata = sc.datasets.pbmc68k_reduced()
cp.partition(adata, method="camp3", gamma=50, random_state=0)
cp.mt.quality(adata, partition_key="camp", label_key="louvain")[["metacell_id", "size", "purity"]].head()
| metacell_id | size | purity | |
|---|---|---|---|
| 0 | seed0-50-__all__ | 65 | 0.984615 |
| 1 | seed1-50-__all__ | 34 | 0.911765 |
| 2 | seed10-50-__all__ | 3 | 0.666667 |
| 3 | seed11-50-__all__ | 158 | 0.708861 |
| 4 | seed12-50-__all__ | 42 | 0.809524 |
For raw counts, run campmc.preprocess() first so obsm['X_pca'] is available.
Installation
Install with pip install campmc (or from a clone for development).
User guide
Workflow overview, CAMP1–4 methods, and AnnData keys.
Tutorials
Walk through partitioning on Scanpy example datasets.
API reference
Functions in pp, tl, mt, and related modules.