2023
Thinking process templates for constructing data stories with SCDNEY
Cao Y, Tran A, Kim H, Robertson N, Lin Y, Torkel M, Yang P, Patrick E, Ghazanfar S, Yang J. Thinking process templates for constructing data stories with SCDNEY. F1000Research 2023, 12: 261. DOI: 10.12688/f1000research.130623.1.Peer-Reviewed Original Research
2020
CiteFuse enables multi-modal analysis of CITE-seq data
Kim H, Lin Y, Geddes T, Yang J, Yang P. CiteFuse enables multi-modal analysis of CITE-seq data. Bioinformatics 2020, 36: 4137-4143. PMID: 32353146, DOI: 10.1093/bioinformatics/btaa282.Peer-Reviewed Original ResearchConceptsCITE-seq dataLigand-receptor interaction analysisCell surface proteinsMulti-modal profilingProtein expression analysisLigand-receptor interactionsCell hashingDifferential RNATranscriptome dataDistinct speciesCellular indexingExpression analysisDoublet detectionIntegrative analysisMolecular biologyStreamlined packageTranscriptomeSingle cellsInteractive web-based visualizationSupplementary dataRNAR packageProfilingEpitope profilesSuite of tools
2019
Evaluating stably expressed genes in single cells
Lin Y, Ghazanfar S, Strbenac D, Wang A, Patrick E, Lin D, Speed T, Yang J, Yang P. Evaluating stably expressed genes in single cells. GigaScience 2019, 8: giz106. PMID: 31531674, PMCID: PMC6748759, DOI: 10.1093/gigascience/giz106.Peer-Reviewed Original ResearchConceptsSingle-cell levelScRNA-seq datasetsHousekeeping genesExpression stabilitySingle-cell RNA-seq profilingSingle cellsSingle-cell transcriptomesRNA-seq profilingSubset of genesDiverse biological systemsBioconductor R packageCell population levelEssential functionsStable expressionGenesIndividual cellsData normalizationTissue typesCell populationsDifferent cellsPopulation levelR packageBiological systemsCellsPotential role