Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-spatial-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Spatial transcriptomics: alignment → deconvolution → domain detection.

OpenClawNanoClawAnalysisReproductionbio-workflows-spatial-pipeline🧠 bioos extended suitebioos extended bioinformatics suitespatial

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-spatial-pipeline

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

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow for analyzing Visium, Xenium, or other spatial transcriptomics data.
adata = sq.read.visium('spaceranger_output/').

Source Doc

Excerpt From SKILL.md

Step 1: Load Data

import scanpy as sc
import squidpy as sq
import numpy as np
import matplotlib.pyplot as plt

## Or load from specific files

adata = sc.read_10x_h5('filtered_feature_bc_matrix.h5')
adata.uns['spatial'] = ...  # Add spatial info

## For Xenium

adata = sq.read.xenium('xenium_output/')

print(f'Loaded: {adata.n_obs} spots/cells, {adata.n_vars} genes')

Use cases

Use bio-workflows-spatial-pipeline for genomics and bioinformatics workflows.
Apply bio-workflows-spatial-pipeline to sequencing, variant, or omics analysis tasks.