RT Journal Article SR Electronic T1 Orchestrating Single-Cell Analysis with Bioconductor JF bioRxiv FD Cold Spring Harbor Laboratory SP 590562 DO 10.1101/590562 A1 Robert A. Amezquita A1 Vince J. Carey A1 Lindsay N. Carpp A1 Ludwig Geistlinger A1 Aaron T. L. Lun A1 Federico Marini A1 Kevin Rue-Albrecht A1 Davide Risso A1 Charlotte Soneson A1 Levi Waldron A1 Hervé Pagès A1 Mike Smith A1 Wolfgang Huber A1 Martin Morgan A1 Raphael Gottardo A1 Stephanie C. Hicks YR 2019 UL http://biorxiv.org/content/early/2019/03/27/590562.abstract AB Recent developments in experimental technologies such as single-cell RNA sequencing have enabled the profiling a high-dimensional number of genome-wide features in individual cells, inspiring the formation of large-scale data generation projects quantifying unprecedented levels of biological variation at the single-cell level. The data generated in such projects exhibits unique characteristics, including increased sparsity and scale, in terms of both the number of features and the number of samples. Due to these unique characteristics, specialized statistical methods are required along with fast and efficient software implementations in order to successfully derive biological insights. Bioconductor - an open-source, open-development software project based on the R programming language - has pioneered the analysis of such high-throughput, high-dimensional biological data, leveraging a rich history of software and methods development that has spanned the era of sequencing. Featuring state-of-the-art computational methods, standardized data infrastructure, and interactive data visualization tools that are all easily accessible as software packages, Bioconductor has made it possible for a diverse audience to analyze data derived from cutting-edge single-cell assays. Here, we present an overview of single-cell RNA sequencing analysis for prospective users and contributors, highlighting the contributions towards this effort made by Bioconductor.