Evidence claim

Scanpy: description

Description of Scanpy

Python toolkit for single-cell gene expression analysis, with methods for preprocessing, visualisation, clustering, trajectory inference and differential expression testing.

Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

14 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field description Context-only references	scFoundation primary supplement, Table4 Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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 Retrieved: 2026-09-23T11:36:02.116209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `9ef9ed1b87014fb72b22cfc99a5382b01e6a6395a0c5de36921d155848162ae1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	Abstract: SCANPY: large-scale single-cell gene expression data analysis Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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/29409532 (title and abstract), Genome biology 2018 Retrieved: 2026-10-11T00:59:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `2ccec8651e795ef20410dda5c5d8d0010be3cb02f3b5f697c5e5404165bc6fdb` 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. Inspected artifact
Previous value Scanpy cell-type annotation pipeline reported in the primary table; fitting/configuration details unextracted. Context-only references	scFoundation primary supplement, Table4 Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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 Retrieved: 2026-09-23T11:36:02.116209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `9ef9ed1b87014fb72b22cfc99a5382b01e6a6395a0c5de36921d155848162ae1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Scanpy cell-type annotation pipeline reported in the primary table; fitting/configuration details unextracted. Context-only references	Abstract: SCANPY: large-scale single-cell gene expression data analysis Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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/29409532 (title and abstract), Genome biology 2018 Retrieved: 2026-10-11T00:59:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `2ccec8651e795ef20410dda5c5d8d0010be3cb02f3b5f697c5e5404165bc6fdb` 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. Inspected artifact
Source location qa-descriptions-20261011-b-source-scanpy: abstractText; coverage-source-scfoundation-supp: Supplementary Table 4 Context-only references	scFoundation primary supplement, Table4 Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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 Retrieved: 2026-09-23T11:36:02.116209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `9ef9ed1b87014fb72b22cfc99a5382b01e6a6395a0c5de36921d155848162ae1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location qa-descriptions-20261011-b-source-scanpy: abstractText; coverage-source-scfoundation-supp: Supplementary Table 4 Context-only references	Abstract: SCANPY: large-scale single-cell gene expression data analysis Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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/29409532 (title and abstract), Genome biology 2018 Retrieved: 2026-10-11T00:59:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `2ccec8651e795ef20410dda5c5d8d0010be3cb02f3b5f697c5e5404165bc6fdb` 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. Inspected artifact
Claimed value Python toolkit for single-cell gene expression analysis, with methods for preprocessing, visualisation, clustering, trajectory inference and differential expression testing. Context-only references	scFoundation primary supplement, Table4 Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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 Retrieved: 2026-09-23T11:36:02.116209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `9ef9ed1b87014fb72b22cfc99a5382b01e6a6395a0c5de36921d155848162ae1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value Python toolkit for single-cell gene expression analysis, with methods for preprocessing, visualisation, clustering, trajectory inference and differential expression testing. Context-only references	Abstract: SCANPY: large-scale single-cell gene expression data analysis Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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/29409532 (title and abstract), Genome biology 2018 Retrieved: 2026-10-11T00:59:01Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `2ccec8651e795ef20410dda5c5d8d0010be3cb02f3b5f697c5e5404165bc6fdb` 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. Inspected artifact
Description Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value. Context-only references	scFoundation primary supplement, Table4 Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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 Retrieved: 2026-09-23T11:36:02.116209+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `9ef9ed1b87014fb72b22cfc99a5382b01e6a6395a0c5de36921d155848162ae1` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value. Context-only references	Abstract: SCANPY: large-scale single-cell gene expression data analysis Original source ↗ qa-descriptions-20261011-b-source-scanpy: abstractText; 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/29409532 (title and abstract), Genome biology 2018 Retrieved: 2026-10-11T00:59:01Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `2ccec8651e795ef20410dda5c5d8d0010be3cb02f3b5f697c5e5404165bc6fdb` 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. Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · 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: SCANPY: large-scale single-cell gene expression data analysis · Original source · Europe PMC core record MED/29409532 (title and abstract), Genome biology 2018

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Technical metadata and extraction receipts

Stable ID: metadata-correction-0f6d91cf5529b04b7b06

areas: single-cell
field: description
previous value: Scanpy cell-type annotation pipeline reported in the primary table; fitting/configuration details unextracted.
value: Python toolkit for single-cell gene expression analysis, with methods for preprocessing, visualisation, clustering, trajectory inference and differential expression testing.
source locator: qa-descriptions-20261011-b-source-scanpy: abstractText; coverage-source-scfoundation-supp: Supplementary Table 4
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude integrator agent for issue #88. Reviewer: a separate Claude review agent, independent of the extractor; no human review claimed.; date: 2026-10-11; method note: Compared the store diff with origin/main, read each new description against its cited source passage and checked the licence of each new source record.; note: Approved. 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.; receipt: data/omics/qa-descriptions-20261011-b/review.json

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subject: Scanpy

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