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1.
Cell Syst ; 9(4): 383-392.e6, 2019 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-31521605

RESUMO

Single-cell computational pipelines involve two critical steps: organizing cells (clustering) and identifying the markers driving this organization (differential expression analysis). State-of-the-art pipelines perform differential analysis after clustering on the same dataset. We observe that because clustering "forces" separation, reusing the same dataset generates artificially low p values and hence false discoveries. We introduce a valid post-clustering differential analysis framework, which corrects for this problem. We provide software at https://github.com/jessemzhang/tn_test.


Assuntos
Biologia Computacional/métodos , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Análise por Conglomerados , Conjuntos de Dados como Assunto , Perfilação da Expressão Gênica , Humanos , Viés de Seleção , Software
2.
BMC Bioinformatics ; 19(1): 93, 2018 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-29523077

RESUMO

BACKGROUND: With the recent proliferation of single-cell RNA-Seq experiments, several methods have been developed for unsupervised analysis of the resulting datasets. These methods often rely on unintuitive hyperparameters and do not explicitly address the subjectivity associated with clustering. RESULTS: In this work, we present DendroSplit, an interpretable framework for analyzing single-cell RNA-Seq datasets that addresses both the clustering interpretability and clustering subjectivity issues. DendroSplit offers a novel perspective on the single-cell RNA-Seq clustering problem motivated by the definition of "cell type", allowing us to cluster using feature selection to uncover multiple levels of biologically meaningful populations in the data. We analyze several landmark single-cell datasets, demonstrating both the method's efficacy and computational efficiency. CONCLUSION: DendroSplit offers a clustering framework that is comparable to existing methods in terms of accuracy and speed but is novel in its emphasis on interpretabilty. We provide the full DendroSplit software package at https://github.com/jessemzhang/dendrosplit .


Assuntos
Bases de Dados Genéticas , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Algoritmos , Análise por Conglomerados , Humanos , Leucócitos Mononucleares/metabolismo , Padrões de Referência , Software
3.
Genome Biol ; 17(1): 112, 2016 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-27230763

RESUMO

Current approaches to single-cell transcriptomic analysis are computationally intensive and require assay-specific modeling, which limits their scope and generality. We propose a novel method that compares and clusters cells based on their transcript-compatibility read counts rather than on the transcript or gene quantifications used in standard analysis pipelines. In the reanalysis of two landmark yet disparate single-cell RNA-seq datasets, we show that our method is up to two orders of magnitude faster than previous approaches, provides accurate and in some cases improved results, and is directly applicable to data from a wide variety of assays.


Assuntos
Perfilação da Expressão Gênica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de RNA/métodos , Análise de Célula Única/métodos , Animais , Córtex Cerebral/metabolismo , Análise por Conglomerados , Hipocampo/metabolismo , Humanos , Camundongos , Mioblastos/metabolismo
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