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
TC
tcga-bulk-data-preprocessing-with-omicverse
Maintainer FreedomIntelligence · Last updated April 1, 2026
Follow this skill to recreate the preprocessing routine from [`t_tcga.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/t_tcga.ipynb). It automates loading TCGA downloads, generating raw/normalised matrices, initialising metadata, and running survival analyses through `ov.bulk.pyTCGA`.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tcga-preprocessing
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Follow this skill to recreate the preprocessing routine from t_tcga.ipynb. It automates loading TCGA downloads, generating raw/normalised matrices, initialising metadata, and running survival analyses through ov.bulk.pyTCGA.
- Confirm the user has:.
- gdc_sample_sheet.<date>.tsv from the TCGA Sample Sheet export.
- The decompressed gdc_download_xxxxx directory containing expression archives.
- The clinical.cart.<date> directory with clinical XML/JSON files.
Source Doc
Excerpt From SKILL.md
Examples
- "Read my TCGA OV download, initialise metadata, and plot MYC survival curves using DESeq-normalised counts."
- "Reload a saved AnnData file, attach survival annotations, and export the updated
.h5ad." - "Run survival analysis for all genes and store the enriched dataset."
Use cases
- Use tcga-bulk-data-preprocessing-with-omicverse for single-cell or spatial omics analysis.
- Apply tcga-bulk-data-preprocessing-with-omicverse to clustering, integration, or trajectory workflows.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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