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spruce (version 0.99.1)

Spatial Random Effects Clustering of Single Cell Data

Description

Allows for identification of cell sub-populations within tissue samples using Bayesian multivariate mixture models with spatial random effects to account for a wide range of spatial gene expression patterns, as described in Allen et. al, 2021 . Bayesian inference is conducted using efficient Gibbs sampling implemented using 'Rcpp'.

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Version

Install

install.packages('spruce')

Monthly Downloads

34

Version

0.99.1

License

GPL (>= 2)

Maintainer

Carter Allen

Last Published

February 21st, 2022

Functions in spruce (0.99.1)

fit_msn_smooth

Spatial multivariate skew normal mixture model clustering
build_knn_graph

Make KNN network
fit_msn

Multivariate skew-normal mixture model clustering
fit_mvn_MCAR

Multivariate normal spatial mixture model clustering
fit_mvn

Multivariate normal mixture model clustering
fit_mvn_PG_CAR

Multivariate normal mixture model clustering - PG multinom regression w/ CAR random effect
coords_df_sim

stx Mouse brain coordinates
fit_mvn_PG

Multivariate normal mixture model clustering - PG multinom regression
fit_msn_PG_smooth

Multivariate skew normal mixture model clustering - PG multinom regression Spatial smoothing
fit_mvn_PG_CAR_MCAR

Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities
fit_mvn_PG_smooth

Multivariate normal mixture model clustering - PG multinom regression Spatial smoothing
get_map

Get MAP estimate of cluster indicators
fit_spruce

Fit spruce Bayesian spatial mixture model
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
get_scores

Calculate cluster uncertainty
get_psi_sums

Sum all neighboring psis
fit_mvn_smooth

Spatial multivariate normal mixture model clustering
psi_sums

Sum neighboring psis in spot i
plot_deltas

Plot delta parameters from multinomial regression model
fit_mvn_PG_MCAR

Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities
spruce

SPRUCE
fit_mvn_PG_MCAR_smooth

Multivariate normal spatial mixture model clustering w/ PG multinomial regression on membership probabilities and spatial smoothing
remap_canonical2

Canonical re-mapping of mixture component labels