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An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data.

ABSTRACT: Single-cell RNA sequencing (scRNA-seq) has emerged as a popular method to profile gene expression at the resolution of individual cells. While there have been methods and software specifically developed to analyze scRNA-seq data, they are most accessible to users who program. We have created a scRNA-seq clustering analysis GenePattern Notebook that provides an interactive, easy-to-use interface for data analysis and exploration of scRNA-Seq data, without the need to write or view any code. The notebook provides a standard scRNA-seq analysis workflow for pre-processing data, identification of sub-populations of cells by clustering, and exploration of biomarkers to characterize heterogeneous cell populations and delineate cell types.

SUBMITTER: Mah CK

PROVIDER: S-EPMC6611141 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data.

Mah Clarence K CK Wenzel Alexander T AT Juarez Edwin F EF Tabor Thorin T Reich Michael M MM Mesirov Jill P JP

F1000Research 20180816

Single-cell RNA sequencing (scRNA-seq) has emerged as a popular method to profile gene expression at the resolution of individual cells. While there have been methods and software specifically developed to analyze scRNA-seq data, they are most accessible to users who program. We have created a scRNA-seq clustering analysis GenePattern Notebook that provides an interactive, easy-to-use interface for data analysis and exploration of scRNA-Seq data, without the need to write or view any code. The n ...[more]

PMID: 31316748

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