# Finding spatially relevant marker genes in image based spatial transcriptomics data

## Documentation for package ‘jazzPanda’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

jazzPanda-package | jazzPanda: A hybrid approach to find spatially relevant marker genes in image-based spatial transcriptomics data
.check_binning | helper function to check the input of binning
.check_valid_input | helper function to check the inputs passed to marker detection function
.check_valid_names | helper function to check the names of gene/cluster/sample
.compute_observation | Compute observation statistic for permutation framework
.compute_permutation | Compute permutation statistics for permutation framework
.convert_data | Convert SingleCellExperiment/SpatialExperiment/SpatialFeatureExperiment objects to list object for jazzPanda.
.create_cor_mg_result | Create a marker gene result object for correlation approach
.create_lm_mg_result | Create a marker gene result object for linear modelling approach
.get_cluster_vectors | Create spatial vectors for clusters
.get_gene_vectors_cm | Create spatial vectors for genes from count matrix and cell coordinates
.get_gene_vectors_tr | Create spatial vectors for genes from transcript coordinates
.get_lasso_coef | help function to get lasso coefficient for every cluster for a given model
compute_permp | Calculate a p-value for correlation with permutation.
create_genesets | Convert the coordinates of set of genes into vectors.
get_cor | Get observed correlation cor_mg_result
get_full_mg | Get full lasso result from glm_mg_result
get_perm_adjp | Get permutation adjusted p value from cor_mg_result
get_perm_p | Get permutation p value from cor_mg_result
get_top_mg | Get top lasso result from glm_mg_result
get_vectors | Vectorise the spatial coordinates
jazzPanda | jazzPanda: A hybrid approach to find spatially relevant marker genes in image-based spatial transcriptomics data
lasso_markers | Find marker genes with spatial coordinates
rep1_clusters | Rep1 selected cells
rep1_neg | Rep1 negative control genes within the selected region.
rep1_sub | A small section of Xenium human breast cancer rep1.
rep2_clusters | Rep2 selected cells
rep2_neg | Rep2 negative control genes within the selected region.
rep2_sub | A small section of Xenium human breast cancer rep2.