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GenomicsSingle-cellMediumSeedKnown

Cell-type annotation of an unlabeled single-cell atlas

Cluster a single-cell dataset and assign cell-type labels matching an expert reference.

Dr. Marco Bellini
Single-Cell Genomics Lab
A reference atlas of human immune cells
Nature · 2023
~3 h
registered 2025-08-01
single-cellclusteringannotation

End goal

Reach ≥ 0.85 adjusted Rand index vs. the expert annotation.

Overview

Quality-control, normalize, cluster, and annotate a single-cell expression matrix, then score label agreement against an expert-curated reference annotation.

Tools allowed

1
Scanpy·Terminal

Workflow

1-step protocol

Each step is verified against the scientist's targets. Open any simulation to test it live.

  1. 1

    Cluster & annotate

    Step 1 / 1

    Cluster cells and assign types from marker genes.

    Protocol

    1. aQC and normalize.
    2. bLeiden cluster and embed.
    3. cAssign types from markers.

    Targets

    Label agreement≥0.85ARI
    Expected output

    An annotated cell × type assignment.

    Simulations · click to test