| name | clustering-degs |
| description | Find differentially expressed genes (markers) for clusters using wilcoxon, t-test, or logistic regression. Includes consensus markers and resolution scanning. |
| allowed-tools | Read, Bash |
| compatibility | scRNA-seq, snRNA-seq |
Clustering Differential Expression
When to Use
After clustering to identify marker genes for each cluster, or before annotation to refine cluster resolution.
Functions
find_markers(adata, groupby, method="wilcoxon", top_n=20) -> dict
Finds DEGs per cluster.
Parameters:
method: "wilcoxon" (default), "t-test", or "logreg"top_n: number of top markers per cluster
Returns dict keyed by cluster ID with list of gene names.
consensus_markers(adata, groupby, methods=("wilcoxon", "t-test"), min_methods=2, top_n=20) -> dict
Finds markers that appear in results from multiple statistical methods.
Parameters:
methods: tuple of methods to comparemin_methods: minimum number of methods that must agree (default 2)
Returns dict of consensus markers per cluster.
resolution_scan(adata, resolutions, cluster_key="leiden", quality_fn="silhouette") -> dict
Scans multiple resolution values and returns quality scores.
Returns {resolution: score} dict and recommends best resolution.
