Finding spatially relevant marker genes in image based spatial transcriptomics data

[Up] [Top]

Documentation for package ‘jazzPanda’ version 1.0.0

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.