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SkillsMP has collected 496 skills from zja2004/BGI-CLI. Open a skill to review its source and details.
zja2004/BGI-CLIShowing 40 of 496 collected skills.
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural…
Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically,…
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper…
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
Trauma-informed AI moderator for addiction recovery communities. Applies harm reduction principles, honors 12-step traditions, distinguishes healthy conflict from abuse, detects crisis posts. Activate on 'community moderation', 'moderate forum', 'review…
Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and…
Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3)…
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.
Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network…
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing…
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure,…
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML…
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting…
Local Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count .h5ad.
RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory…
This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction,…
Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive…
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap),…
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any…
Orchestrate multi-simulation campaigns including parameter sweeps, batch jobs, and result aggregation. Use for running parameter studies, managing simulation batches, tracking job status, combining results from multiple runs, or automating simulation…
Validate simulations before, during, and after execution. Use for pre-flight checks, runtime monitoring, post-run validation, diagnosing failed simulations, checking convergence, detecting NaN/Inf, or verifying mass/energy conservation.
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or…
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
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.
Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.
Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
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.
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.
Generate SLURM `sbatch` job scripts and sanity-check HPC resource requests (nodes, tasks, CPUs, memory, GPUs) for simulation runs. Use when preparing submission scripts, deciding MPI vs MPI+OpenMP layouts, standardizing `#SBATCH` directives, or debugging job…
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.
Expert speech-language pathologist specializing in AI-powered speech therapy, phoneme analysis, articulation visualization, voice disorders, fluency intervention, and assistive communication technology. Activate on 'speech therapy', 'articulation', 'phoneme…
Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research.
Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.