Bulk Linking Analysis for Single-cell Experiments
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Documentation for package ‘blase’ version 0.99.3
Help Pages
| annotate_sce | Annotate a SCE with BLASE Mappings |
| as.BlaseData | Conversion to BlaseData |
| as.BlaseData-method | Conversion to BlaseData |
| assign_pseudotime_bins | Assign Pseudotime Bins to a source object's metadata |
| assign_pseudotime_bins-method | Assign Pseudotime Bins to a source object's metadata |
| best_bin | Get best bin of a BLASE Mapping Results object. |
| best_bin-method | Get best bin of a BLASE Mapping Results object. |
| best_correlation | Get best correlation of a BLASE Mapping Results object. |
| best_correlation-method | Get best correlation of a BLASE Mapping Results object. |
| BlaseData | Blase Data Object |
| BlaseData-class | Blase Data Object |
| bootstrap_iterations | Get the number of bootstrap iterations performed for a BLASE Mapping Results object. |
| bootstrap_iterations-method | 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. |
| bulk_name-method | Get name of bulk of a BLASE Mapping Results object. |
| calculate_gene_peakedness | calculate_gene_peakedness |
| confident_mapping | Get if the result is confident for a BLASE Mapping Results object. |
| confident_mapping-method | Get if the result is confident for a BLASE Mapping Results object. |
| 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 |
| genes | Get genes of a BLASE Data object. |
| genes-method | Get genes of a BLASE Data object. |
| genes<- | Set genes of a BLASE Data object. |
| genes<--method | Set genes of a BLASE Data object. |
| gene_peakedness_spread_selection | Gene Peakedness Spread Selection |
| get_bins_as_bulk | Get a pseudobulk of bins with at least 2 replicates |
| get_top_n_genes | Get Top Genes From An AssociationTestResult |
| MappingResult | Blase Mapping Result |
| MappingResult-class | Blase Mapping Result |
| mapping_history | Get the mapping history for a BLASE Mapping Results object. |
| mapping_history-method | Get the mapping history for a BLASE Mapping Results object. |
| 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 |
| MCA_PF_SCE | Malaria Cell Atlas Plasmodium falciparum for BLASE Vignette |
| painter_microarray | Painter 2018 Plasmodium falciparum 48h asexual lifecycle microarray data |
| plot_bin_population | Plot the populations of a bin |
| plot_bin_population-method | Plot the populations of a bin |
| plot_find_best_params_results | Plot the results of the search for good parameters |
| plot_gene_peakedness | plot_gene_peakedness |
| plot_mapping_result | Plot a summary of the mapping result |
| plot_mapping_result-method | 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 |
| show-method | Show an MappingResult object |
| show-method | Show an BlaseData object |
| smooth_gene | smooth_gene |
| top_2_distance | Get the difference in correlation between the top 2 most correlated bins for a BLASE Mapping Results object. |
| top_2_distance-method | Get the difference in correlation between the top 2 most correlated bins for a BLASE Mapping Results object. |
| tradeSeq_BLASE_example_sce | TradeSeq Example SCE for BLASE Vignette |
| zhang_2021_heat_shock_bulk | Zhang 2021 Plasmodium falciparum heat shock bulk data |