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ASAP: a Web-based platform for the analysis and inter-active visualization of single-cell RNA-seq data

By Vincent Gardeux, Fabrice David, Adrian Shajkofci, Petra C Schwalie, Bart Deplancke

Posted 22 Dec 2016
bioRxiv DOI: 10.1101/096222 (published DOI: 10.1093/bioinformatics/btx337)

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 repre-sentation 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 analy-sis 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 anal-ysis workflows, ASAP should conceptually be broadly applicable to any RNA-seq dataset. As a validation, we demon-strate 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.ch

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