bulktrajblend-trajectory-interpolation
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-trajblend-interpolation --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.
# BulkTrajBlend trajectory interpolation ## Overview Invoke this skill when users need to bridge gaps in single-cell developmental trajectories using matched bulk RNA-seq. It follows [`t_bulktrajblend.ipynb`](../../omicverse_guide/docs/Tutorials-bulk2single/t_bulktrajblend.ipynb), showcasing how BulkTrajBlend deconvolves PDAC bulk samples, identifies overlapping communities with a GNN, and interpolates "interrupted" cell states. ## Instructions 1. **Prepare libraries and inputs** - Import `omicverse as ov`, `scanpy as sc`, `scvelo as scv`, and helper functions like `from omicverse.utils import mde`; run `ov.plot_set()`. - Load the reference scRNA-seq AnnData (`scv.datasets.dentategyrus()`) and raw bulk counts with `ov.utils.read(...)` followed by `ov.bulk.Matrix_ID_mapping(...)` for gene ID harmonisation. 2. **Configure BulkTrajBlend** - Instantiate `ov.bulk2single.BulkTrajBlend(bulk_seq=bulk_df, single_seq=adata, bulk_group=['dg_d_1','dg_d_2','dg_d_3'], celltype_key='clusters')`. - Explain that `bulk_group` names correspond to raw bulk columns and the method expects unscaled counts. 3. **Set beta-VAE expectations** - Call `bulktb.vae_configure(cell_target_num=100)` (or pass a dict
- Overview
- Instructions
- Examples
- References
What does the bulktrajblend-trajectory-interpolation skill do?
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating missing states.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-trajblend-interpolation --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.