TY - JOUR
T1 - ASAP 2020 update
T2 - An open, scalable and interactive web-based portal for (single-cell) omics analyses
AU - David, Fabrice P.A.
AU - Litovchenko, Maria
AU - Deplancke, Bart
AU - Gardeux, Vincent
N1 - Funding Information:
Chan Zuckerberg Initiative (CZI) grant for collaborative computational tools [2018-182612 (5022)]; Precision Health & related Technologies grant [PHRT-502]; Swiss National Science Foundation (SNSF) project grant [310030 182655]; institutional support by the EPFL (Open Science Fund). Funding for open access charge: Open Science fund from the EPFL. The open access publication charge for this paper has been waived by Oxford University Press – NAR Editorial Board members are entitled to one free paper per year in recognition of their work on behalf of the journal. Conflict of interest statement. None declared.
Publisher Copyright:
© 2020 Oxford University Press. All rights reserved.
PY - 2021
Y1 - 2021
N2 - Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in 'big data' management, forcing researchers to stay up to speed with increasingly complex analytical processes and rapidly evolving methods. To render these processes and approaches more accessible, we developed the webbased, collaborative portal ASAP (Automated Singlecell Analysis Portal). Our primary goal is thereby to democratize single-cell omics data analyses (scRNAseq and more recently scATAC-seq). By taking advantage of a Docker system to enhance reproducibility, and novel bioinformatics approaches that were recently developed for improving scalability, ASAP meets challenging requirements set by recent cell atlasing efforts such as the Human (HCA) and Fly (FCA) Cell Atlas Projects. Specifically, ASAP can now handle datasets containing millions of cells, integrating intuitive tools that allow researchers to collaborate on the same project synchronously. ASAP tools are versioned, and researchers can create unique access IDs for storing complete analyses that can be reproduced or completed by others. Finally, ASAP does not require any installation and provides a full and modular single-cell RNA-seq analysis pipeline. ASAP is freely available at https://asap.epfl.ch.
AB - Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in 'big data' management, forcing researchers to stay up to speed with increasingly complex analytical processes and rapidly evolving methods. To render these processes and approaches more accessible, we developed the webbased, collaborative portal ASAP (Automated Singlecell Analysis Portal). Our primary goal is thereby to democratize single-cell omics data analyses (scRNAseq and more recently scATAC-seq). By taking advantage of a Docker system to enhance reproducibility, and novel bioinformatics approaches that were recently developed for improving scalability, ASAP meets challenging requirements set by recent cell atlasing efforts such as the Human (HCA) and Fly (FCA) Cell Atlas Projects. Specifically, ASAP can now handle datasets containing millions of cells, integrating intuitive tools that allow researchers to collaborate on the same project synchronously. ASAP tools are versioned, and researchers can create unique access IDs for storing complete analyses that can be reproduced or completed by others. Finally, ASAP does not require any installation and provides a full and modular single-cell RNA-seq analysis pipeline. ASAP is freely available at https://asap.epfl.ch.
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U2 - 10.1093/NAR/GKAA412
DO - 10.1093/NAR/GKAA412
M3 - Article
C2 - 32449934
AN - SCOPUS:85087320189
SN - 0305-1048
VL - 48
SP - W403-W414
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - W1
ER -