cellconsensus 1.2.0

Hierarchical unsupervised cell type annotation from consensus markers

CellConsensus

⚠️ Heavy development. API and outputs are evolving rapidly — breaking changes between versions should be expected. Pin a specific version if you need stability.

Hierarchical unsupervised cell type annotation from consensus marker genes — three levels of granularity, no reference atlas required, plus user-defined gene-set and cell-type scoring.

📖 Full README with figures and demo video: https://github.com/tansey-lab/cellconsensus

Explore the database

Browse the underlying consensus marker database — per-cell-type marker lists, sources, and gene rankings — at http://cellconsensus.org/.

The same database is exposed as an MCP server so AI assistants can query it conversationally (e.g. "what are the markers for memory CD8+ T cells?", "what is the cell type for this set of marker genes: LST1, FCER1G, AIF1, FTH1, IFITM2?"):

https://wrbcaolmpdeefznfkqpj.supabase.co/functions/v1/mcp

Claude: Settings → Connectors → Add custom connector → paste the URL above. ChatGPT: Settings → Apps → Advanced settings → enable Developer mode → Create Connector → paste the URL above.

Installation

pip install cellconsensus

Or the latest development version from GitHub:

pip install git+https://github.com/tansey-lab/cellconsensus.git

Usage

from cellconsensus import CellConsensus
import anndata as ad

adata = ad.read_h5ad("my_data.h5ad")

cc = CellConsensus()
cc.fit(adata, include_cancer=True, cancer_types=["lung_adenocarcinoma"])

labels_lvl1 = cc.predict(level=1)   # "T cell", "myeloid cell", ...
labels_lvl2 = cc.predict(level=2)   # "CD4+ T cell", "macrophage", ...
labels_lvl3 = cc.predict(level=3)   # "memory CD4+ T cell", ...

# Per-cell × per-type score matrix (DataFrame, n_cells x n_lvl1_types)
S = cc.score_matrix(level=1)

# Save / reload
cc.save("model.pkl")
cc2 = CellConsensus.load("model.pkl")

cancer_types accepts any key from cellconsensus.list_cancer_types() (120 entries including lung_adenocarcinoma, breast_carcinoma, melanoma, …). Omit include_cancer for normal-tissue-only fits. The available cell-type keys at each level are listed by cellconsensus.load_cell_type(level=1|2|3).

Per-cell-type scores

predict_score returns the continuous score for any cell type (at any level) or any cancer type, reduced the same way as fit (NN smoothing for ccc, per-cluster averaging for precomputed). Use load_cell_type(level=N) to see the available cell-type keys; list_cancer_types() for cancer keys.

from cellconsensus import load_cell_type, list_cancer_types

load_cell_type(level=1)   # {'t_cell': 'T cell', 'myeloid_cell': 'myeloid cell', ...}
load_cell_type(level=2)   # 44 subtypes
load_cell_type(level=3)   # 76 fine-grained types

# Single key, list, or mixed cell type + cancer in one call:
cc.predict_score("t_cell")                       # L1 T-cell score per cell
cc.predict_score(["nk", "monocyte"], level=2)    # two L2 scores
cc.predict_score(["t_cell", "melanoma"])         # mixed; cancer auto-detected

Custom gene signatures

Score cells against any user-supplied marker list — pooled the same way as the built-in references (NN-graph smoothing for ccc, per-cluster averaging for precomputed), so the result is directly comparable to entries of score_matrix.

sig = {"WT1": 10, "CCND1": 8, "CD99": 7, "NCAM1": 6, "MKI67": 5}
df = cc.predict_gene_set(list(sig.keys()), weights=sig, name="my_sig")
adata.obs["my_sig_score"] = df["my_sig"].values

weights accepts a list, a dict (missing entries default to 1.0), or None for uniform. Negative weights are allowed (anti-markers).

Bringing your own clusters

Already have clusters (Leiden, or anything else)? Pass clustering="precomputed" with the obs column that holds the labels. CellConsensus uses the same three-level taxonomy as the default ccc mode — it just averages the marker scores across all cells in each cluster (no NN smoothing) and labels every cluster by the argmax. Clusters are never split: each one gets a single label per level, gaining precision from level 1 to level 3.

import scanpy as sc

sc.pp.neighbors(adata)
sc.tl.leiden(adata, key_added="my_clusters")   # your clustering, your way

cc = CellConsensus(clustering="precomputed", cluster_key="my_clusters")
cc.fit(adata)
cc.predict(level=1)   # "T cell", "myeloid cell", ...
cc.predict(level=3)   # "memory CD4+ T cell", ...