ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells Article Swipe
Andrew Jiang
,
Russell G. Snell
,
Klaus Lehnert
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btae167
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btae167
Motivation In recent years, improvements in throughput of single-cell RNA-seq have resulted in a significant increase in the number of cells profiled. The generation of single-cell RNA-seq datasets comprising >1 million cells is becoming increasingly common, giving rise to demands for more efficient computational workflows. Results We present an update to our single-cell RNA-seq analysis web server application, ICARUS (available at https://launch.icarus-scrnaseq.cloud.edu.au) that allows effective analysis of large-scale single-cell RNA-seq datasets. ICARUS v3 utilizes the geometric cell sketching method to subsample cells from the overall dataset for dimensionality reduction and clustering that can be then projected to the large dataset. We then extend this functionality to select a representative subset of cells for downstream data analysis applications including differential expression analysis, gene co-expression network construction, gene regulatory network construction, trajectory analysis, cell–cell communication inference, and cell cluster associations to GWAS traits. We demonstrate analysis of single-cell RNA-seq datasets using ICARUS v3 of 1.3 million cells completed within the hour. Availability and implementation ICARUS is available at https://launch.icarus-scrnaseq.cloud.edu.au.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btae167
- https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae167/57105701/btae167.pdf
- OA Status
- gold
- Cited By
- 4
- References
- 20
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4393276283
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4393276283Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bioinformatics/btae167Digital Object Identifier
- Title
-
ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cellsWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
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2024Year of publication
- Publication date
-
2024-03-25Full publication date if available
- Authors
-
Andrew Jiang, Russell G. Snell, Klaus LehnertList of authors in order
- Landing page
-
https://doi.org/10.1093/bioinformatics/btae167Publisher landing page
- PDF URL
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https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae167/57105701/btae167.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae167/57105701/btae167.pdfDirect OA link when available
- Concepts
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ICARUS, Computer science, Single-cell analysis, Scalability, Cloud computing, Inference, Computational biology, Cell, Biology, Database, Artificial intelligence, Operating system, Genetics, Particle physics, PhysicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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4Total citation count in OpenAlex
- Citations by year (recent)
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2025: 3, 2024: 1Per-year citation counts (last 5 years)
- References (count)
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20Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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