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02_int_clustering.default.yaml
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02_int_clustering.default.yaml
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CLUSTER_GRAPH_LEIDEN_ENABLED: True
CLUSTER_GRAPH_LOUVAIN_ENABLED: True
CLUSTER_GRAPH_WALKTRAP_ENABLED: True
CLUSTER_KMEANS_K_ENABLED: True
CLUSTER_KMEANS_KBEST_ENABLED: True
CLUSTER_SC3_ENABLED: True
CLUSTER_SC3_N_CORES: 8
CELL_ANNOTATION_SOURCES:
- human_primary_cell_atlas_main:
reference_type: "celldex"
reference: "HumanPrimaryCellAtlasData"
description: >
Microarray datasets derived from human primary cells (Mabbott et al. 2013).
Most of the labels refer to blood subpopulations but cell types from other tissues are also available.
label_column: "label.main"
label_subsets: []
train_params:
de_method: "wilcox"
de_n: 30
monaco_immune_main:
reference_type: "celldex"
reference: "MonacoImmuneData"
description: "This is the human immune reference that best covers all of the bases for a typical PBMC sample."
label_column: "label.main"
label_subsets: []
train_params:
genes: "sd"
CELL_GROUPINGS:
- cluster_int_graph_louvain_r0.4_annotated:
source_column: "cluster_int_graph_louvain_r0.4"
description: "Graph-based clustering (Louvain alg.), annotated clusters"
assignments:
1: "memory_CD4+"
6: "B"
7: "memory_CD4+"
INT_CLUSTERING_REPORT_DIMRED_PLOTS_OTHER:
- "phase": "Cell cycle phases"
"batch": "Batch of origin"
"doublet_score": "Doublet score"
"total": "Total number of UMI"
"detected": "Detected number of genes"
"cluster_quickcluster": "Graph-based clustering for integration diagnostics."
"cluster_int_graph_louvain_r0.4_annotated": null