AN
Data & Repro
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observation metadata (obs)…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
SI
single-cell-preprocessing-with-omicverse
Maintainer FreedomIntelligence · Last updated April 1, 2026
Follow this skill when a user needs to reproduce the preprocessing workflow from the omicverse notebooks [`t_preprocess.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb), [`t_preprocess_cpu.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb), and [`t_preprocess_gpu.ipynb`](../../omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb). The tutorials operate on the 1….
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-preprocessing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Follow this skill when a user needs to reproduce the preprocessing workflow from the omicverse notebooks t_preprocess.ipynb, t_preprocess_cpu.ipynb, and t_preprocess_gpu.ipynb. The tutorials operate on the 10x PBMC3k dataset and cover QC filtering, normalisation, highly variable gene (HVG) detection, dimensionality reduction, and downstream embeddings.
- if 'batch' not in adata.obs.columns: adata.obs['batch'] = 'batch_1' # Default single batch.
Source Doc
Excerpt From SKILL.md
Overview
Follow this skill when a user needs to reproduce the preprocessing workflow from the omicverse notebooks t_preprocess.ipynb, t_preprocess_cpu.ipynb, and t_preprocess_gpu.ipynb. The tutorials operate on the 10x PBMC3k dataset and cover QC filtering, normalisation, highly variable gene (HVG) detection, dimensionality reduction, and downstream embeddings.
Use cases
- Use single-cell-preprocessing-with-omicverse for single-cell or spatial omics analysis.
- Apply single-cell-preprocessing-with-omicverse to clustering, integration, or trajectory workflows.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Related skills
Related skills
AR
Data & Repro
Arboreto
Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using paralleli.
K-Dense-AI/claude-scientific-skillsView
BI
Data & Repro
bio-imaging-mass-cytometry-cell-segmentation
Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cel…
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-read-qc-umi-processing
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and ac…
FreedomIntelligence/OpenClaw-Medical-SkillsView