Package index
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BlaseData-classBlaseData - Blase Data Object
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as.BlaseData() - Conversion to BlaseData
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assign_pseudotime_bins() - Assign Pseudotime Bins to a source object's metadata
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genes() - Get genes of a BLASE Data object.
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`genes<-`() - Set genes of a BLASE Data object.
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show(<BlaseData>) - Show an BlaseData object
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MappingResult() - Blase Mapping Result
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`bulk_name<-`() - Set name of bulk of a BLASE Mapping Results object.
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best_bin() - Get best bin of a BLASE Mapping Results object.
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best_correlation() - Get best correlation of a BLASE Mapping Results object.
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bootstrap_iterations() - Get the number of bootstrap iterations performed for a BLASE Mapping Results object.
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bulk_name() - Get name of bulk of a BLASE Mapping Results object.
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mapping_history() - Get the mapping history for a BLASE Mapping Results object.
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metric() - Get the mapping history for a BLASE Mapping Results object.
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strong_mapping() - Get if the result is strong for a BLASE Mapping Results object.
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top_2_distance() - Get the difference in correlation between the top 2 most correlated bins for a BLASE Mapping Results object.
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show(<MappingResult>) - Show an MappingResult object
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map_all_best_bins() - Map many bulk samples in the same dataframe
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map_best_bin() - Map the best matching SC bin for a bulk sample
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plot_bin_population() - Plot the populations of a bin
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plot_mapping_result() - Plot a summary of the mapping result
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plot_mapping_result_corr() - Plot a mapping result's correlation
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plot_mapping_result_heatmap() - Plot a mapping result heatmap
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evaluate_parameters() - Evaluate n_bins and n_genes for bin mapping
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evaluate_top_n_genes() - Evaluate Top Genes
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find_best_params() - Identify the Best Parameters For Your Dataset
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plot_find_best_params_results() - Plot the results of the search for good parameters
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calculate_gene_peakedness() - calculate_gene_peakedness
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gene_peakedness_spread_selection() - Gene Peakedness Spread Selection
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get_top_n_genes() - Get Top Genes From An AssociationTestResult
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plot_gene_peakedness() - plot_gene_peakedness
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smooth_gene() - smooth_gene
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annotate_sce() - Annotate a SCE with BLASE Mappings
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get_bins_as_bulk() - Get a pseudobulk of bins with at least 2 replicates
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MCA_PF_SCE - Malaria Cell Atlas Plasmodium falciparum for BLASE Vignette
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painter_microarray - Painter 2018 Plasmodium falciparum 48h asexual lifecycle microarray data
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tradeSeq_BLASE_example_sce - TradeSeq Example SCE for BLASE Vignette
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zhang_2021_heat_shock_bulk - Zhang 2021 Plasmodium falciparum heat shock bulk data