Mar 12, 2016

FastProject: A Tool for Low-Dimensional Analysis of Single-Cell RNA-Seq Data

BioRxiv : the Preprint Server for Biology
David DeTomaso, Nir Yosef

Abstract

Background: A key challenge in the emerging field of single-cell RNA-Seq is to characterize phenotypic diversity between cells and visualize this information in an informative manner. A common technique when dealing with high-dimensional data is to project the data to 2 or 3 dimensions for visualization. However, there are a variety of methods to achieve this result and once projected, it can be difficult to ascribe biological significance to the observed features. Additionally, when analyzing single-cell data, the relationship between cells can be obscured by technical confounders such as variable gene capture rates. Results: To aid in the analysis and interpretation of single-cell RNA-Seq data, we have developed FastProject, a software tool which analyzes a gene expression matrix and produces a dynamic output report in which two-dimensional projections of the data can be explored. Annotated gene sets (referred to as gene 'signatures') are incorporated so that features in the projections can be understood in relation to the biological processes they might represent. FastProject provides a novel method of scoring each cell against a gene signature so as to minimize the effect of missed transcripts as well as a method to rank si...Continue Reading

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Mentioned in this Paper

Single-Cell Analysis
Computer Software
Projection Defense Mechanism
2-Dimensional
Genes
Projections and Predictions
Research Project
Gene Expression
2D Echocardiography
Composite Architecture

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