Package index • blase

BLASE Object

BlaseData-class BlaseData: Blase Data Object

as.BlaseData(): Conversion to BlaseData

assign_pseudotime_bins(): Assign Pseudotime Bins to a source object's metadata

genes(): Get genes of a BLASE Data object.

`genes<-`(): Set genes of a BLASE Data object.

show(<BlaseData>): Show an BlaseData object

BLASE Mapping Result Object

MappingResult-class MappingResult: Blase Mapping Result

best_bin(): Get best bin of a BLASE Mapping Results object.

best_correlation(): Get best correlation of a BLASE Mapping Results object.

bootstrap_iterations(): Get the number of bootstrap iterations performed for a BLASE Mapping Results object.

bulk_name(): Get name of bulk of a BLASE Mapping Results object.

confident_mapping(): Get if the result is confident for a BLASE Mapping Results object.

mapping_history(): Get the mapping history for a BLASE Mapping Results object.

top_2_distance(): Get the difference in correlation between the top 2 most correlated bins for a BLASE Mapping Results object.

show(<MappingResult>): Show an MappingResult object

Mapping Bulks

map_all_best_bins(): Map many bulk samples in the same dataframe

map_best_bin(): Map the best matching SC bin for a bulk sample

Plots

plot_bin_population(): Plot the populations of a bin

plot_mapping_result(): Plot a summary of the mapping result

plot_mapping_result_corr(): Plot a mapping result's correlation

plot_mapping_result_heatmap(): Plot a mapping result heatmap

Parameter Tuning

evaluate_parameters(): Evaluate n_bins and n_genes for bin mapping

evaluate_top_n_genes(): Evaluate Top Genes

find_best_params(): Identify the Best Parameters For Your Dataset

plot_find_best_params_results(): Plot the results of the search for good parameters

Gene Selection

calculate_gene_peakedness(): calculate_gene_peakedness

gene_peakedness_spread_selection(): Gene Peakedness Spread Selection

get_top_n_genes(): Get Top Genes From An AssociationTestResult

plot_gene_peakedness(): plot_gene_peakedness

smooth_gene(): smooth_gene

Annotation of scRNA-seq

annotate_sce(): Annotate a SCE with BLASE Mappings

Utilities

get_bins_as_bulk(): Get a pseudobulk of bins with at least 2 replicates