LiteratureScientific Writing & PublishingFreedomIntelligence/OpenClaw-Medical-SkillsLiterature Review

bio-machine-learning-atlas-mapping

Maintainer FreedomIntelligence · Last updated April 1, 2026

Map query cells to reference atlases with scANVI or Symphony.

OpenClawNanoClawDiscoveryReadingbio-machine-learning-atlas-mapping🧠 bioos extended suitebioos extended bioinformatics suitemap

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-machine-learning-atlas-mapping

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

adata_ref = sc.read_h5ad('reference.h5ad').
scvi.model.SCVI.setup_anndata(adata_ref, layer='counts', batch_key='batch') ref_model = scvi.model.SCVI.load('reference_model/', adata=adata_ref).

Source Doc

Excerpt From SKILL.md

scVI Reference Mapping (scArches)

import scvi
import scanpy as sc

## Prepare query data

adata_query = sc.read_h5ad('query.h5ad')

## Subset to reference genes

adata_query = adata_query[:, adata_ref.var_names].copy()

Use cases

Use bio-machine-learning-atlas-mapping for manuscript drafting and submission workflows.
Apply bio-machine-learning-atlas-mapping when polishing research communication outputs.