CellTypist
Machine-learning tool for rapid cell-type annotation of single-cell RNA-seq data.
2 evaluations · 2 results2 configurations with further results
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Sorted by Macro F1 (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 2 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: CellTypist | Protocol: scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation Dataset subset: Segerstolpe subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split) | 0.812 Macro F1 fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceCell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Aggregation: Not reported scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16, row CellTypist, column Segerstolpe |
| Pipeline: CellTypist | Protocol: scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Dataset subset: Zheng68K subset used in scFoundation Supplementary Table4 (scFoundation cell-type annotation comparison split) | 0.725 Macro F1 fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Evaluation origin not reported · Source checkedMethods, coverage and sourceCellTypist on scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation Cell-type annotation evaluated by unweighted mean of cell-type F1 scores. Each class F1=TP/(TP+0.5*(FP+FN)), defined in Supplementary Note3. Exact dataset release, split manifest, fitting and preprocessing remain unextracted. Aggregation: Not reported scFoundation primary supplement, Table4 · Supplementary Table4, PDF p16, row CellTypist, column Zheng68K |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
Further results on linked records
2 linked records have results that are not included above, because no reviewed claim yet ties the link to this pipeline. Each record keeps its own settings and evaluations, and its scores are on its own page.
- CellTypist — scTab Table 1 Configuration · configuration of this pipeline · 3 evaluations · 4 results
- celltypist default parameters — scTab Table 6 Configuration · configuration of this pipeline · 1 evaluation · 1 result
Use this pipeline
How it works, versions and access
Additional methodological details, versions and access terms have not yet been extracted into a structured profile for this pipeline. Consult the linked sources and evaluation records below.
Evidence
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Evidence table
Inspect claims, sources and review details
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Machine-learning tool for rapid cell-type annotation of single-cell RNA-seq data. Individual claims | scFoundation primary supplement, Table4 qa-descriptions-20261011-b-source-celltypist: abstractText ('CellTypist, a machine learning tool for rapid and precise cell type annotation'); coverage-source-scfoundation-supp: Supplementary Table 4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41592-024-02305-7 publisher supplement | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the new sources' licences against the arXiv abstract pages and Europe PMC, the 7 scFoundation pipeline descriptions against their abstracts, the language-model descriptions against their model cards and reports, and the TAPE architecture figures against the TAPE paper; all correct. The catalogue entries reuse reviewed profile summaries. Field: Claim: metadata-correction-f689d7513a540218deeb Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Description Machine-learning tool for rapid cell-type annotation of single-cell RNA-seq data. Individual claims | Abstract: Cross-tissue immune cell analysis reveals tissue-specific features in humans (CellTypist) qa-descriptions-20261011-b-source-celltypist: abstractText ('CellTypist, a machine learning tool for rapid and precise cell type annotation'); coverage-source-scfoundation-supp: Supplementary Table 4 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/35549406 (title and abstract), Science 2022 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the new sources' licences against the arXiv abstract pages and Europe PMC, the 7 scFoundation pipeline descriptions against their abstracts, the language-model descriptions against their model cards and reports, and the TAPE architecture figures against the TAPE paper; all correct. The catalogue entries reuse reviewed profile summaries. Field: Claim: metadata-correction-f689d7513a540218deeb Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records and release history
- scFoundation primary supplement, Table4 · Original source · 10.1038/s41592-024-02305-7 publisher supplement
- Abstract: Cross-tissue immune cell analysis reveals tissue-specific features in humans (CellTypist) · Original source · Europe PMC core record MED/35549406 (title and abstract), Science 2022
Technical metadata and extraction receipts
Stable ID: scfoundation-2024-supp-table4-method-celltypist
- areas
- single-cell
- source locator
- Supplementary Table4, PDF p16, row CellTypist
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
Related records
- subject: CellTypist: description
- system: CellTypist on scFoundation cell-type annotation comparison Segerstolpe: Segerstolpe cell-type annotation
- system: CellTypist on scFoundation cell-type annotation comparison Zheng68K: Zheng68K cell-type annotation
- configuration of: CellTypist — scTab Table 1
- configuration of: celltypist default parameters — scTab Table 6