bulk-rna-seq-deconvolution-with-bulk2single
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-to-single-deconvolution --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.
# Bulk RNA-seq deconvolution with Bulk2Single ## Overview Use this skill when a user wants to reconstruct single-cell profiles from bulk RNA-seq together with a matched reference scRNA-seq atlas. It follows [`t_bulk2single.ipynb`](../../omicverse_guide/docs/Tutorials-bulk2single/t_bulk2single.ipynb), which demonstrates how to harmonise PDAC bulk replicates, train the beta-VAE generator, and benchmark the output cells against dentate gyrus scRNA-seq. ## Instructions 1. **Load libraries and data** - Import `omicverse as ov`, `scanpy as sc`, `scvelo as scv`, `anndata`, and `matplotlib.pyplot as plt`, then call `ov.plot_set()` to match omicverse styling. - Read the bulk counts table with `ov.read(...)`/`ov.utils.read(...)` and harmonise gene identifiers via `ov.bulk.Matrix_ID_mapping(<df>, 'genesets/pair_GRCm39.tsv')`. - Load the reference scRNA-seq AnnData (e.g., `scv.datasets.dentategyrus()`) and confirm the cluster labels (stored in `adata.obs['clusters']`). 2. **Initialise the Bulk2Single model** - Instantiate `ov.bulk2single.Bulk2Single(bulk_data=bulk_df, single_data=adata, celltype_key='clusters', bulk_group=['dg_d_1', 'dg_d_2', 'dg_d_3'], top_marker_num=200, ratio_num=1, gpu=0)`
- Overview
- Instructions
- Examples
- References
What does the bulk-rna-seq-deconvolution-with-bulk2single skill do?
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-to-single-deconvolution --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.