Package index • scdown

Main workflows

scdown(): Create a scdown object
summarize_dataset(): Summarize dataset structure
plot_map(): Plot cluster or annotation maps
find_markers(): Find marker genes for each annotation
check_annotation(): Check annotation with known marker panels
plot_average_expression(): Plot average expression by annotation
plot_cluster_similarity(): Plot similarity between annotations
plot_signature(): Plot signature or pathway scores
infer_communication(): Infer exploratory cell-cell communication
run_core(): Run the minimal downstream workflow
build_scdown_report(): Build a compact HTML report

Inputs and example data

scdown_example(): Example annotated scRNA-seq dataset

Built-in resources

immune_signatures(): Built-in immune signatures
immune_marker_panels(): Built-in immune marker panels
list_signatures(): List available signatures
get_signature(): Get one signature