2020
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Lin Y, Cao Y, Kim H, Salim A, Speed T, Lin D, Yang P, Yang J. scClassify: sample size estimation and multiscale classification of cells using single and multiple reference. Molecular Systems Biology 2020, 16: msb199389. PMID: 32567229, PMCID: PMC7306901, DOI: 10.15252/msb.20199389.Peer-Reviewed Original ResearchConceptsType hierarchyKey computational challengeType identificationMultiple referencesType classification methodMultiscale classificationEnsemble learningCell type hierarchyClassification frameworkClassification methodPairs of referenceJoint classificationComputational challengesAccurate classificationLarge collectionTesting dataArt methodologiesDatasetLevel of complexityExperimental datasetsCell type identificationClassificationSingle-cell atlasesNovel applicationScalability
2019
scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets
Lin Y, Ghazanfar S, Wang K, Gagnon-Bartsch J, Lo K, Su X, Han Z, Ormerod J, Speed T, Yang P, Yang J. scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 9775-9784. PMID: 31028141, PMCID: PMC6525515, DOI: 10.1073/pnas.1820006116.Peer-Reviewed Original ResearchConceptsMultiple single-cell RNA-seq datasetsSingle-cell RNA-seq datasetsRNA-seq datasetsSingle-cell RNA sequencing dataRNA sequencing dataFurther biological insightsBiological discoveryBiological insightsSequencing dataStable expressionConcerted examinationRobust data integrationLarge collectionIndividual datasetsGenesMultiple collectionsPseudoreplicatesExpression