BioDSH

In the author's own words, from each skill's SKILL.md.

• anova-designs

  在只能使用 numpy/scipy/pandas 时计算平衡或不平衡析因 ANOVA 的 I/II/III 型平方和、随机区组与裂区的多误差层 ANOVA、完整重复测量 ANOVA、单随机截距 REML 和等权估计边际均值。需要复现 R aov(Error(...)) 的 SS/df/MS/F/p、选择正确整区/亚区分母，或避免把缺失格和对比编码处理错时使用；实现经 R car、nlme、emmeans 逐项验证。

  biodsh-core/skills/anova-designs/SKILL.md on GitHub (opens in a new tab)

• bulk-rnaseq-limma-voom

  Bulk RNA-seq differential expression with limma-voom (and edgeR TMM) in plain Python/numpy/scipy, matching R limma; use for count matrices (including fractional RSEM expected counts) with covariates, moderated t statistics, empirical Bayes prior df/variance, voom weights or LOWESS mean-variance trends when R is unavailable.

  biodsh-core/skills/bulk-rnaseq-limma-voom/SKILL.md on GitHub (opens in a new tab)

• data-format-bridge

  Convert analysis tables (csv/tsv/xlsx/parquet/h5ad obs-var/rds/sav/dta) into the formats clinicians and statisticians open directly — SPSS .sav, Stata .dta, R .rds with a ready-to-run .R script, GraphPad Prism .pzfx plus a Prism-ready wide CSV, and tidy Excel workbooks. Never touches the input file.

  biodsh-core/skills/data-format-bridge/SKILL.md on GitHub (opens in a new tab)

• desktop-control

  See and drive the user's desktop without vision - list and focus windows, read on-screen controls and text as JSON with coordinates (UI Automation on Windows, OCR elsewhere), then click, type, send hotkeys, open apps and paste tables into Excel/SPSS/GraphPad Prism/Zotero.

  biodsh-core/skills/desktop-control/SKILL.md on GitHub (opens in a new tab)

• drug-docking

  Virtual screening by molecular docking with AutoDock Vina — dock a set of small-molecule ligands (given as SMILES in a .smi/.csv/.txt file, or as an .sdf) into a receptor pocket, rank the hits by predicted binding affinity (kcal/mol) and save the best pose for each ligand. Use for structure-based drug screening / hit finding, not for ligand-based similarity search.

  biodsh-core/skills/drug-docking/SKILL.md on GitHub (opens in a new tab)

• image-generate

  Generate scientific illustrations (graphical abstracts, mechanism schematics, cover art, poster art) from a text prompt through the image provider configured in the BioDSH app. Not for data plots.

  biodsh-core/skills/image-generate/SKILL.md on GitHub (opens in a new tab)

• md-simulation

  Run a short molecular dynamics simulation of a protein (optionally a protein-ligand complex) with OpenMM — fix the structure, minimize, equilibrate, run a brief production trajectory, and report backbone RMSD stability over time. Use to relax/equilibrate a structure and check its stability, not for long production MD or free-energy calculations.

  biodsh-core/skills/md-simulation/SKILL.md on GitHub (opens in a new tab)

• pipeline-builder

  Turn a completed BioDSH task, or an existing analysis procedure someone else wrote (script, notebook, Snakefile/Nextflow, methods text), into a reproducible, re-runnable workflow through a guided plan the user confirms step by step, with user-chosen validation checks; writes pipelines/<id>/pipeline.json plus step scripts and verifies a clean re-run.

  biodsh-core/skills/pipeline-builder/SKILL.md on GitHub (opens in a new tab)

• regression-robust-se

  OLS/WLS and logistic or Poisson regression with HC0-HC3 heteroskedasticity-robust SEs, one-way cluster CR0/CR1/CR1S and Bell–McCaffrey CR2, explicit Wald/t/normal inference and bread/meat diagnostics in numpy/scipy/pandas; use when R or statsmodels is unavailable and robust covariance conventions must match R sandwich, clubSandwich and lmtest.

  biodsh-core/skills/regression-robust-se/SKILL.md on GitHub (opens in a new tab)

• scanpy-clustering

  Run a minimal deterministic Scanpy pipeline (QC, normalization, HVG, PCA, Leiden clustering, UMAP) on an h5ad file and write clusters.csv, umap.png and summary.json.

  biodsh-core/skills/scanpy-clustering/SKILL.md on GitHub (opens in a new tab)

• scrna-cellstate-annotation

  Assign evidence-backed broad immune cell classes and T-cell states to clustered AnnData data without using clinical outcome labels.

  biodsh-core/skills/scrna-cellstate-annotation/SKILL.md on GitHub (opens in a new tab)

• scrna-inspect-qc

  Inspect an input AnnData h5ad file and produce auditable single-cell RNA-seq quality-control evidence without modifying or filtering the source data.

  biodsh-core/skills/scrna-inspect-qc/SKILL.md on GitHub (opens in a new tab)

• scrna-preprocess-cluster

  Preprocess and cluster an AnnData h5ad dataset with state-aware normalization, deterministic Scanpy settings, and machine-readable scientific provenance.

  biodsh-core/skills/scrna-preprocess-cluster/SKILL.md on GitHub (opens in a new tab)

• scrna-repro-audit

  Read-only reproducibility audit of a completed BioDSH run bundle: verifies input/command/output hashes and result consistency from a result.json.

  biodsh-core/skills/scrna-repro-audit/SKILL.md on GitHub (opens in a new tab)

• scrna-treatment-response

  Compare immune-cell compositions between response groups using patient-level aggregation, deterministic inference, and explicit longitudinal-label safeguards.

  biodsh-core/skills/scrna-treatment-response/SKILL.md on GitHub (opens in a new tab)

• scrna-virtual-knockout

  In-silico single-gene knockout on scRNA-seq (scTenifoldKnk-style): build a gene regulatory network, virtually knock out a gene, and rank the genes most affected by its loss.

  biodsh-core/skills/scrna-virtual-knockout/SKILL.md on GitHub (opens in a new tab)

• survival-km-cox

  Analyse right-censored time-to-event data using Kaplan–Meier, log/log-log Greenwood confidence intervals, ordinary or stratified log-rank tests, Breslow/Efron Cox regression with stratification and cluster-robust covariance, baseline hazards, individual survival curves, and RMST differences in numpy/scipy/pandas when R is unavailable. Validated numerically against R survival and survRM2.

  biodsh-core/skills/survival-km-cox/SKILL.md on GitHub (opens in a new tab)

• zotero-connect

  Read and extend the user's own Zotero 7 library through the local desktop app — search papers, list collections and tags, pull PDF full text for summarising, add references by DOI/PMID, and export BibTeX/RIS/CSL-JSON. Never deletes or edits existing items.

  biodsh-core/skills/zotero-connect/SKILL.md on GitHub (opens in a new tab)

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