ASAP: A web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

Vincent Gardeux, Fabrice P.A. David, Adrian Shajkofci, Petra C. Schwalie, Bart Deplancke

Research output: Research - peer-reviewArticle

Abstract

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 datasets. 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.

LanguageEnglish (US)
Pages3123-3125
Number of pages3
JournalBioinformatics
Volume33
Issue number19
DOIs
StatePublished - 2017

Fingerprint

Web-based
Visualization
Cell
Single-Cell Analysis
RNA
Pipelines
Genes
RNA Sequence Analysis
Sequencing
Gene
Datasets
Expertise
Tissue
Workflow
Information Storage and Retrieval
Gene Expression Profiling
Multigene Family
Research Personnel
Genome
Research

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

ASAP : A web-based platform for the analysis and interactive visualization of single-cell RNA-seq data. / Gardeux, Vincent; David, Fabrice P.A.; Shajkofci, Adrian; Schwalie, Petra C.; Deplancke, Bart.

In: Bioinformatics, Vol. 33, No. 19, 2017, p. 3123-3125.

Research output: Research - peer-reviewArticle

Gardeux, V, David, FPA, Shajkofci, A, Schwalie, PC & Deplancke, B 2017, 'ASAP: A web-based platform for the analysis and interactive visualization of single-cell RNA-seq data' Bioinformatics, vol 33, no. 19, pp. 3123-3125. DOI: 10.1093/bioinformatics/btx337
Gardeux, Vincent ; David, Fabrice P.A. ; Shajkofci, Adrian ; Schwalie, Petra C. ; Deplancke, Bart. / ASAP : A web-based platform for the analysis and interactive visualization of single-cell RNA-seq data. In: Bioinformatics. 2017 ; Vol. 33, No. 19. pp. 3123-3125
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