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BlackSheep: A Bioconductor and Bioconda Package for Differential Extreme Value Analysis.
Blumenberg, Lili; Kawaler, Emily A; Cornwell, MacIntosh; Smith, Shaleigh; Ruggles, Kelly V; Fenyö, David.
Afiliação
  • Blumenberg L; Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York 10016, United States.
  • Kawaler EA; Division of Translational Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, New York 10016, United States.
  • Cornwell M; Institute for Systems Genetics, New York University Grossman School of Medicine, New York, New York 10016, United States.
  • Smith S; Vilcek Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, New York 10016, United States.
  • Ruggles KV; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York 10016, United States.
  • Fenyö D; Institute for Systems Genetics, New York University Grossman School of Medicine, New York, New York 10016, United States.
J Proteome Res ; 20(7): 3767-3773, 2021 07 02.
Article em En | MEDLINE | ID: mdl-34165986
ABSTRACT
Unbiased assays such as shotgun proteomics and RNA-seq provide high-resolution molecular characterization of tumors. These assays measure molecules with highly varied distributions, making interpretation and hypothesis testing challenging. Samples with the most extreme measurements for a molecule can reveal the most interesting biological insights yet are often excluded from analysis. Furthermore, rare disease subtypes are, by definition, underrepresented in cancer cohorts. To provide a strategy for identifying molecules aberrantly enriched in small sample cohorts, we present BlackSheep, a package for nonparametric description and differential analysis of genome-wide data, available from Bioconductor (https//www.bioconductor.org/packages/release/bioc/html/blacksheepr.html) and Bioconda (https//bioconda.github.io/recipes/blksheep/README.html). BlackSheep is a complementary tool to other differential expression analysis methods, which is particularly useful when analyzing small subgroups in a larger cohort.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Genoma Idioma: En Ano de publicação: 2021 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Genoma Idioma: En Ano de publicação: 2021 Tipo de documento: Article