# Bulk Linking Analysis for Single-cell Experiments

## Documentation for package ‘blase’ version 1.1.2

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

## 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.
bulk_name<- | Set name of bulk of a BLASE Mapping Results object.
bulk_name<--method | Set name of bulk of a BLASE Mapping Results object.
calculate_gene_peakedness | calculate_gene_peakedness
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
metric | Get the mapping history for a BLASE Mapping Results object.
metric-method | Get the mapping history for a BLASE Mapping Results object.
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
strong_mapping | Get if the result is strong for a BLASE Mapping Results object.
strong_mapping-method | Get if the result is strong 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.
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