RT Journal Article SR Electronic T1 ASAP: A web-based platform for the analysis and interactive visualization of single-cell RNA-seq data JF bioRxiv FD Cold Spring Harbor Laboratory SP 096222 DO 10.1101/096222 A1 Vincent Gardeux A1 Fabrice David A1 Adrian Shajkofci A1 Petra C. Schwalie A1 Bart Deplancke YR 2016 UL http://biorxiv.org/content/early/2016/12/22/096222.abstract AB Motivation Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet, these groups often lack the expertise to handle complex scRNA-seq data sets.Results We developed a fully integrated, web-based platform aimed at the complete analysis of scRNA-seq data post genome alignment: from the parsing, filtering, and normalization of the input count data files, to the visual representation of the data, identification of cell clusters, differentially expressed genes (including cluster-specific marker genes), and functional gene set enrichment. This Automated Single-cell Analysis Pipeline (ASAP) combines a wide range of commonly used algorithms with sophisticated visualization tools. Compared with existing scRNA-seq analysis platforms, researchers (including those lacking computational expertise) are able to interact with the data in a straightforward fashion and in real time. Furthermore, given the overlap between scRNA-seq and bulk RNA-seq analysis workflows, ASAP should conceptually be broadly applicable to any RNA-seq dataset. As a validation, we demonstrate how we can use ASAP to simply reproduce the results from a single-cell study of 91 mouse cells involving five distinct cell types.Availability The tool is freely available at http://asap.epfl.chContact bart.deplancke{at}epfl.ch