tcga-bulk-data-preprocessing-with-omicverse
Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill tcga-preprocessing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# TCGA bulk data preprocessing with omicverse ## Overview 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`. ## Instructions 1. **Gather required downloads** - 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. - Mention that sample data are available under [`omicverse_guide/docs/Tutorials-bulk/data/TCGA_OV/`](../../omicverse_guide/docs/Tutorials-bulk/data/TCGA_OV/). 2. **Initialise the TCGA helper** - Import `omicverse as ov` (and `scanpy as sc` if plotting) then call `ov.plot_set()`. - Instantiate `aml_tcga = ov.bulk.pyTCGA(sample_sheet_path, download_dir, clinical_dir)`. - Run `aml_tcga.adata_init()` to build the AnnData object with raw counts, FPKM, and TPM layers. 3. **Persist the dataset** - Encourage saving the initial AnnData: `aml_tcga.adata.write_h5ad('da
- Overview
- Instructions
- Examples
- References
What does the tcga-bulk-data-preprocessing-with-omicverse skill do?
Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill tcga-preprocessing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.