數據與 AI

Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.

Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.

Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.

Creates event-driven email listeners that monitor for specific conditions (like urgent emails from boss, newsletters to archive, package tracking) and execute custom actions. Use when user wants to be notified about emails, automatically handle certain emails, or set up email automation workflows.

Help Claude query STRING for protein interactions, build PPI graphs with pyPPI, and render styled network figures for bulk gene lists.

Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).

Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.

Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.

Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.

Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.

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.

Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.

Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.

Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes.

Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.

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.

Expert Java developer skill for AgentScope Java framework - a reactive, message-driven multi-agent system built on Project Reactor. Use when working with reactive programming, LLM integration, agent orchestration, multi-agent systems, or when the user mentions AgentScope, ReActAgent, Mono/Flux, Project Reactor, or Java agent development. Specializes in non-blocking code, tool integration, hooks, pipelines, and production-ready agent applications.

Morning routine, midday check-in, and evening shutdown workflows. Structure daily planning, task review, and end-of-day reflection. Use for daily productivity routines.

Read and write Obsidian vault files, manage wiki-links, process markdown with YAML frontmatter. Use when working with vault file operations, creating notes, or managing links.