ai4nucleome

ai4nucleome/BioMaster

Agent Claude CodeOpenCode

Verify BioMaster step outputs, maintain CHECKREPORT.yaml and PROJECTLOG.yaml, and emit structured check results.

ai4nucleome/BioMaster

Agent Claude CodeOpenCode

Inspect BioMaster script execution status and propose bounded retry advice.

ai4nucleome/BioMaster

Agent Claude CodeOpenCode

Execute BioMaster plan steps using only the exec skills referenced by PLAN.yaml.

ai4nucleome/BioMaster

Agent Claude CodeOpenCode

Primary BioMaster agent. Collects goals, selects/reuses a project folder, routes through SQLite, generates PLAN.yaml, and coordinates workers.

ai4nucleome/BioMaster

Agent Claude CodeOpenCode

Skill curator. Evaluates raw material, and (re)divides it into a curated macro/micro + structured-steps BioSkill via the bioskills-author tool.

ai4nucleome/BioMaster

Agent Claude CodeOpenCode

Skill generator. Synthesizes a brand-new curated BioSkill from a paper / URL / GitHub repo plus a required skill-focus description, using webfetch to read source material and the bioskills-author tool to write.

ai4nucleome/BioMaster

Agent Claude CodeOpenCode

Skill router. Decides which BioSkills layer (macro/micro) each sub-agent sees and fetches it via the bioskills tool.

ai4nucleome/BioMaster

Skill OpenCode

Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.

ai4nucleome/BioMaster

Skill OpenCode

Ligand-receptor communication inference in single-cell or spatial data with sender-receiver summaries and cautious interpretation.

ai4nucleome/BioMaster

Skill OpenCode

Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation.

ai4nucleome/BioMaster

Skill OpenCode

Workflow for spatial transcriptomics preprocessing, domain detection, deconvolution, neighborhood analysis, and publication-ready spatial maps.

ai4nucleome/BioMaster

Skill OpenCode

Pseudotime, lineage branching, and state-transition analysis for single-cell data with coherent embeddings and annotations.

ai4nucleome/BioMaster

Skill OpenCode

Standard scRNA-seq preprocessing and clustering with Scanpy: QC, filtering, normalization, HVG selection, PCA, neighbors, UMAP, and Leiden clustering, producing an analysis-ready AnnData object.

ai4nucleome/BioMaster

Skill OpenCode

Router/index skill over 1,676 deduplicated biomedical AI agent skills aggregated from 20 repositories into 15 categories; use it to search the index, locate the best-matching skill, fetch its SKILL.md on demand, and follow it.

ai4nucleome/BioMaster

Skill OpenCode

End-to-end protein binder design via BindCraft AF2 hallucination with built-in validation; runs on Modal or locally and reports per-design QC metrics.

ai4nucleome/BioMaster

Skill OpenCode

Load BioMaster as one integrated skill-driven bioinformatics assistant.

ai4nucleome/BioMaster

Skill OpenCode

Map query scRNA-seq data onto a pre-trained reference atlas via scArches surgical transfer learning (scVI/scANVI) to obtain a shared latent embedding and transferred cell type labels without retraining the reference.

ai4nucleome/BioMaster

Skill OpenCode

Integrate multiple scRNA-seq batches to remove batch effects while preserving biological variation, using Harmony, scVI, Seurat anchors, or fastMNN.

ai4nucleome/BioMaster

Skill OpenCode

Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) into a BioMaster project's bioskills library.

ai4nucleome/BioMaster

Skill OpenCode

Detect and remove doublets from scRNA-seq data using Scrublet (Python), DoubletFinder (R), or scDblFinder (R).

ai4nucleome/BioMaster

Skill OpenCode

Automated cell type annotation for preprocessed single-cell data using reference-based and custom classifiers (CellTypist, SingleR, Azimuth, scPred), with confidence filtering, consensus voting, and marker-based validation.

ai4nucleome/BioMaster

Skill OpenCode

Infer and quantify cell-cell communication from scRNA-seq data using CellChat, NicheNet, and LIANA frameworks.

ai4nucleome/BioMaster

Skill OpenCode

Segment cells from IMC images using Cellpose/Mesmer/steinbock and extract per-cell expression data with spatial coordinates.

ai4nucleome/BioMaster

Skill OpenCode

Integrate multiple histone modification ChIP-seq tracks into chromatin states via ChromHMM (with alternatives Segway, EpiSegMix, IDEAS, EpiLogos, full-stack ChromHMM).