Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data Article Swipe
Piotr Rutkowski
,
Marcin Tabaka
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.10.05.561074
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1101/2023.10.05.561074
The recent expansion of single-cell technologies has enabled simultaneous genome-wide measurements of multiple modalities in the same single cell. The potential to jointly profile such modalities as gene expression, chromatin accessibility, protein epitopes, or multiple histone modifications at single-cell resolution represents a compelling opportunity to study developmental processes at multiple layers of gene regulation. Here, we present Ocelli, a lightweight Python package for scalable visualization and exploration of developmental multimodal single-cell data. The core functionality of Ocelli focuses on diffusion-based modeling of developmental processes. Ocelli addresses common tasks in developmental single-cell data analysis, such as visualization of cells on a low-dimensional embedding that preserves the continuity of the developmental progression of cells, identification of rare and transient cell states, integration with trajectory inference algorithms, and imputation of undetected feature counts. Extensive benchmarking shows that Ocelli outperforms existing methods regarding computational time and quality of the reconstructed low-dimensional representation of developmental data.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2023.10.05.561074
- https://www.biorxiv.org/content/biorxiv/early/2023/10/07/2023.10.05.561074.full.pdf
- OA Status
- green
- Cited By
- 1
- References
- 80
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
Raw OpenAlex JSON
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https://doi.org/10.1101/2023.10.05.561074Digital Object Identifier
- Title
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Ocelli: an open-source tool for the visualization of developmental multimodal single-cell dataWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-10-07Full publication date if available
- Authors
-
Piotr Rutkowski, Marcin TabakaList of authors in order
- Landing page
-
https://doi.org/10.1101/2023.10.05.561074Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2023/10/07/2023.10.05.561074.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2023/10/07/2023.10.05.561074.full.pdfDirect OA link when available
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Visualization, Computer science, Simple eye in invertebrates, Computational biology, Data visualization, Artificial intelligence, Biology, AnatomyTop concepts (fields/topics) attached by OpenAlex
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1Total citation count in OpenAlex
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2025: 1Per-year citation counts (last 5 years)
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80Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.epitopes, | 33 |
| abstract_inverted_index.expansion | 3 |
| abstract_inverted_index.inference | 123 |
| abstract_inverted_index.potential | 21 |
| abstract_inverted_index.preserves | 104 |
| abstract_inverted_index.processes | 48 |
| abstract_inverted_index.regarding | 139 |
| abstract_inverted_index.transient | 117 |
| abstract_inverted_index.compelling | 43 |
| abstract_inverted_index.continuity | 106 |
| abstract_inverted_index.imputation | 126 |
| abstract_inverted_index.modalities | 14, 26 |
| abstract_inverted_index.multimodal | 70 |
| abstract_inverted_index.processes. | 84 |
| abstract_inverted_index.represents | 41 |
| abstract_inverted_index.resolution | 40 |
| abstract_inverted_index.trajectory | 122 |
| abstract_inverted_index.undetected | 128 |
| abstract_inverted_index.algorithms, | 124 |
| abstract_inverted_index.exploration | 67 |
| abstract_inverted_index.expression, | 29 |
| abstract_inverted_index.genome-wide | 10 |
| abstract_inverted_index.integration | 120 |
| abstract_inverted_index.lightweight | 60 |
| abstract_inverted_index.opportunity | 44 |
| abstract_inverted_index.outperforms | 136 |
| abstract_inverted_index.progression | 110 |
| abstract_inverted_index.regulation. | 54 |
| abstract_inverted_index.single-cell | 5, 39, 71, 91 |
| abstract_inverted_index.benchmarking | 132 |
| abstract_inverted_index.measurements | 11 |
| abstract_inverted_index.simultaneous | 9 |
| abstract_inverted_index.technologies | 6 |
| abstract_inverted_index.computational | 140 |
| abstract_inverted_index.developmental | 47, 69, 83, 90, 109, 150 |
| abstract_inverted_index.functionality | 75 |
| abstract_inverted_index.modifications | 37 |
| abstract_inverted_index.reconstructed | 146 |
| abstract_inverted_index.visualization | 65, 96 |
| abstract_inverted_index.accessibility, | 31 |
| abstract_inverted_index.identification | 113 |
| abstract_inverted_index.representation | 148 |
| abstract_inverted_index.diffusion-based | 80 |
| abstract_inverted_index.low-dimensional | 101, 147 |
| cited_by_percentile_year.max | 95 |
| cited_by_percentile_year.min | 91 |
| corresponding_author_ids | https://openalex.org/A5011787284 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 2 |
| corresponding_institution_ids | https://openalex.org/I4210157029, https://openalex.org/I99542240 |
| citation_normalized_percentile.value | 0.60788269 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |