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scIB

scIB measures both batch removal and biological preservation in single-cell integration.

0 evaluations · 0 metric rows

At a glance

Explanatory profile: source reviewed · Automated source review, 2026-09-16. This does not change the review status of its results.

Data, procedure and scoring
PropertyDescription and evidence
Record typeEvaluator and associated benchmarking studytheislab/scib official source · README: Package scib; Metrics; Integration Tools; Resources
InputsSingle-cell expression or chromatin data with batch and biological annotationstheislab/scib official source · README: Package scib; Metrics; Integration Tools; Resources
Outputs and assessmentBiological-conservation and batch-correction metric panelstheislab/scib official source · README: Package scib; Metrics; Integration Tools; Resources
DatasetsNot extracted or verified for this record.
OrganismsNot extracted or verified for this record.
AssaysNot extracted or verified for this record.
SplitsNot extracted or verified for this record.
AdaptationNot extracted or verified for this record.
BaselinesNot extracted or verified for this record.

How it works

Procedure overview

Conceptual overview of the cited procedure; consult the pinned source for executable settings.

Procedure overviewAnnotated cell data. Then: Integrate batches. Then: Measure biological conservation. Then: Measure batch correctionAnnotated cell dataIntegrate batchesMeasure biological conservationMeasure batch correction
Read the diagram as text
  1. Annotated cell data
  2. Integrate batches
  3. Measure biological conservation
  4. Measure batch correction
theislab/scib official source · README: Package scib; Metrics; Integration Tools; Resources

Procedure

Preprocess annotated single-cell data, run an integration method and evaluate its representation. Inspect biological-conservation metrics alongside batch-correction metrics; the package, reusable pipeline and published study are separate resources.

theislab/scib official source · README: Package scib; Metrics; Integration Tools; Resources

Connected tasks and protocols

These associations do not imply identical protocols or interchangeable scores.

Tested models and results

Release 2026-09-16-d74d282221a9 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

Strengths and limitations

Strengths supported by sources

  • Makes the two competing integration objectives visible.theislab/scib official source · README: Package scib; Metrics; Integration Tools; Resources

Limitations and conditions

  • A well-mixed embedding can erase real biological differences; label-dependent scores also depend on the reference annotations.theislab/scib official source · README: Package scib; Metrics; Integration Tools; Resources
Profile review details

Primary-source description checked by an automated research assistant. This is a profile review, not an independent execution or numerical reproduction.

Stable record: discovery-benchmark-scib

Applicable tests and references

Applicability is distinct from a completed evaluation.

Sources and history

Release 2026-09-16-d74d282221a9 · Record review: discovered

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Technical metadata and extraction receipts

Stable ID: discovery-benchmark-scib

areas
single-cell
entity level
suite
missing metadata
dataset release: unextracted; metric implementation: unextracted; split manifest: unextracted; version: unextracted
scope note
Specialist molecular or omics evaluation; protocol details require review before numerical comparison.
task
Single-cell integration evaluation
version
Not reported
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