Spatial Random Effects Clustering of Single Cell Data

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Documentation for package ‘spruce’ version 0.99.1

• DESCRIPTION file.

Help Pages

build_knn_graph	Make KNN network
coords_df_sim	stx Mouse brain coordinates
fit_msn	Multivariate skew-normal mixture model clustering
fit_msn_PG_smooth	Multivariate skew normal mixture model clustering - PG multinom regression Spatial smoothing
fit_msn_smooth	Spatial multivariate skew normal mixture model clustering
fit_mvn	Multivariate normal mixture model clustering
fit_mvn_MCAR	Multivariate normal spatial mixture model clustering
fit_mvn_PG	Multivariate normal mixture model clustering - PG multinom regression
fit_mvn_PG_CAR	Multivariate normal mixture model clustering - PG multinom regression w/ CAR random effect
fit_mvn_PG_CAR_MCAR	Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities
fit_mvn_PG_CAR_MCAR_smooth	Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities with spatial smoothing
fit_mvn_PG_CAR_smooth	Multivariate normal mixture model clustering - PG multinom regression w/ CAR random effect and spatial smoothing
fit_mvn_PG_MCAR	Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities
fit_mvn_PG_MCAR_smooth	Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities and spatial smoothing
fit_mvn_PG_smooth	Multivariate normal mixture model clustering - PG multinom regression Spatial smoothing
fit_mvn_smooth	Spatial multivariate normal mixture model clustering
fit_spruce	Fit spruce Bayesian spatial mixture model
get_map	Get MAP estimate of cluster indicators
get_psi_sums	Sum all neighboring psis
get_scores	Calculate cluster uncertainty
plot_deltas	Plot delta parameters from multinomial regression model
psi_sums	Sum neighboring psis in spot i
remap_canonical2	Canonical re-mapping of mixture component labels
spruce	SPRUCE