Package: blase 1.3.2

Andrew McCluskey

blase: Bulk Linkage Analysis for Single-cell Experiments

BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments.

Authors:Andrew McCluskey [aut, cre], Toby Kettlewell [aut], Adrian M. Smith [aut], Rhiannon Kundu [aut], David A. Gunn [aut], Thomas D. Otto [aut, ths]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
blase/json (API)

# Install 'blase' in R:
install.packages('blase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/andrewmccluskey-uog/blase/issues

Pkgdown/docs site:https://andrewmccluskey-uog.github.io

Datasets:

On BioConductor:blase-1.3.1(bioc 3.24)blase-1.2.0(bioc 3.23)

transcriptomicssinglecellsequencinggeneexpressiontranscriptionrnaseqtimecoursecellbiologysoftwarecellbasedassays

5.73 score 1 stars 7 scripts 197 downloads 32 exports 179 dependencies

Last updated from:843de9e652. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING264
linux-devel-x86_64OK597
source / vignettesOK1470
linux-release-x86_64OK604
macos-release-arm64OK443
macos-oldrel-arm64OK470
windows-develOK511
windows-releaseOK485
windows-oldrelOK488
wasm-releaseOK236

Exports:annotate_sceas.BlaseDataassign_pseudotime_binsbest_binbest_correlationBlaseDatabootstrap_iterationsbulk_namebulk_name<-calculate_gene_peakednessevaluate_parametersevaluate_top_n_genesfind_best_paramsgene_peakedness_spread_selectiongenesgenes<-get_bins_as_bulkget_top_n_genesmap_all_best_binsmap_best_binmapping_historymetricplot_bin_populationplot_find_best_params_resultsplot_gene_peakednessplot_mapping_resultplot_mapping_result_corrplot_mapping_result_heatmapshowsmooth_genestrong_mappingtop_2_distance

Dependencies:abindaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbootbslibcachemcaToolscliclustercodetoolscommonmarkcowplotcpp11crosstalkcurldata.tableDelayedArraydeldirdigestdotCall64dplyrdqrngevaluatefarverfastDummiesfastmapfitdistrplusFNNfontawesomeformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggbeeswarmggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelistenvlmtestlsamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUInlmeopensslotelparallellypatchworkpbapplypheatmappillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectrarsvdRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscattermoresctransformscuttleSeqinfoSeuratSeuratObjectshinySingleCellExperimentsitmosnowSnowballCsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviporviridisviridisLitewithrxfunxtableXVectoryamlzoo

Assigning bulk RNA-seq to pseudotime
Introduction | Principle | Installing BLASE | Setting up the Single Cell Experiment | Finding the most descriptive genes with tradeSeq | Parameter Tuning for BLASE | Inspect Bin Choice | Inspect Genes Choice | Mapping Bulk Samples to SC with BLASE | Plotting Heatmap of Mappings | Plotting Detailed Correlation Maps | Plotting Summary Plots of Mappings | Session Info
Rendered fromassign-bulk-to-pseudotime.Rmdusingknitr::rmarkdown

Last update: 2026-07-07
Started: 2023-10-27

BLASE for annotating scRNA-seq
Load Data | Prepare BLASE | Create BLASE data object | Select Genes | Calculate Mappings | Transfer Mappings | Session Info
Rendered fromBLASE-for-annotating-scRNA-seq.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-10-01

BLASE for excluding developmental genes from bulk RNA-seq
Load Data | Prepare BLASE | Create BLASE data object | Select Genes | Calculate Mappings | Calculate DE genes | Phenotype + Development (Bulk DE) | Development (SC DE) | Remove Developmental Genes | Session Info
Rendered fromBLASE-for-excluding-developmental-genes-from-bulk-RNA-seq.Rmdusingknitr::rmarkdown

Last update: 2026-02-13
Started: 2025-10-01

Readme and manuals

Help Manual

Help pageTopics
Annotate a SCE with BLASE Mappingsannotate_sce
Conversion to BlaseDataas.BlaseData as.BlaseData,SingleCellExperiment-method
Assign Pseudotime Bins to a source object's metadataassign_pseudotime_bins assign_pseudotime_bins,data.frame-method assign_pseudotime_bins,Seurat-method assign_pseudotime_bins,SingleCellExperiment-method
Get best bin of a BLASE Mapping Results object.best_bin best_bin,MappingResult-method
Get best correlation of a BLASE Mapping Results object.best_correlation best_correlation,MappingResult-method
Blase Data ObjectBlaseData BlaseData-class
Get the number of bootstrap iterations performed for a BLASE Mapping Results object.bootstrap_iterations bootstrap_iterations,MappingResult-method
Get name of bulk of a BLASE Mapping Results object.bulk_name bulk_name,MappingResult-method
Set name of bulk of a BLASE Mapping Results object.bulk_name<- bulk_name<-,MappingResult-method
calculate_gene_peakednesscalculate_gene_peakedness
Evaluate n_bins and n_genes for bin mappingevaluate_parameters
Evaluate Top Genesevaluate_top_n_genes
Identify the Best Parameters For Your Datasetfind_best_params
Gene Peakedness Spread Selectiongene_peakedness_spread_selection
Get genes of a BLASE Data object.genes genes,BlaseData-method
Set genes of a BLASE Data object.genes<- genes<-,BlaseData-method
Get a pseudobulk of bins with at least 2 replicatesget_bins_as_bulk
Get Top Genes From An AssociationTestResultget_top_n_genes
Map many bulk samples in the same dataframemap_all_best_bins
Map the best matching SC bin for a bulk samplemap_best_bin
Get the mapping history for a BLASE Mapping Results object.mapping_history mapping_history,MappingResult-method
Blase Mapping ResultMappingResult MappingResult-class
Malaria Cell Atlas Plasmodium falciparum for BLASE VignetteMCA_PF_SCE
Get the mapping history for a BLASE Mapping Results object.metric metric,MappingResult-method
Painter 2018 Plasmodium falciparum 48h asexual lifecycle microarray datapainter_microarray
Plot the populations of a binplot_bin_population plot_bin_population,SingleCellExperiment-method
Plot the results of the search for good parametersplot_find_best_params_results
plot_gene_peakednessplot_gene_peakedness
Plot a summary of the mapping resultplot_mapping_result plot_mapping_result,SingleCellExperiment,MappingResult-method
Plot a mapping result's correlationplot_mapping_result_corr
Plot a mapping result heatmapplot_mapping_result_heatmap
Show an BlaseData objectshow,BlaseData-method
Show an MappingResult objectshow,MappingResult-method
smooth_genesmooth_gene
Get if the result is strong for a BLASE Mapping Results object.strong_mapping strong_mapping,MappingResult-method
Get the difference in correlation between the top 2 most correlated bins for a BLASE Mapping Results object.top_2_distance top_2_distance,MappingResult-method
TradeSeq Example SCE for BLASE VignettetradeSeq_BLASE_example_sce
Zhang 2021 Plasmodium falciparum heat shock bulk datazhang_2021_heat_shock_bulk