ai4nucleome

Load BioMaster as one integrated skill-driven bioinformatics assistant.

BioMaster conversational bioinformatics assistant; starts workflows only after execution intent or empty activation.

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

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

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

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

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

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.

Use when the user naturally asks to start, continue, monitor, or summarize a GenomeHarness campaign or sequential benchmark suite.

Use when a GenomeHarness v15 campaign has pending PROPOSE requests and proposal JSON must be written from request packets.

Use when a GenomeHarness campaign has a REPAIR request and repair JSON must be written without changing scientific protocol.

Use when generating or reviewing GenomeHarness v15 campaign reports from state.sqlite and trial artifacts.

Use when supervising an official GenomeHarness v15 campaign or sequential suite through the interactive CLI loop.