wu-yc/labclaw

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neurokit2 Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, a…

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omero-integration Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotat…

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openalex-database Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for acad…

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patents-search Search global patents with natural language queries. Prior art, patent landscapes, and innovation tracking via Valyu.

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perplexity-search Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This s…

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polars Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in mem…

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protocol_video_matching Real-time XR video vs. protocol text matching and deviation detection. Aligns first-person XR headset video streams f…

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protocolsio-integration Integration with protocols.io API for managing scientific protocols. This skill should be used when working with prot…

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pubmed-database Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation manageme…

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pydeseq2 Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR co…

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pymc-bayesian-modeling Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, post…

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pytdc Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molec…

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research-grants Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review cr…

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scanpy Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE),…

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scholar-evaluation Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across resear…

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scientific-brainstorming Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary co…

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scikit-learn Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression),…

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tooluniverse-adverse-event-detection Detect and analyze adverse drug event signals using FDA FAERS data, drug labels, disproportionality analysis (PRR, RO…

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tooluniverse-binder-discovery Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates …

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tooluniverse-disease-research Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report fil…

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tooluniverse-immunotherapy-response-prediction Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer typ…

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tooluniverse-literature-deep-research Conduct comprehensive literature research with target disambiguation, evidence grading, and structured theme extracti…

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tooluniverse-multiomic-disease-characterization Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and th…

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tooluniverse-variant-interpretation Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural …

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torch-geometric Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, m…

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uniprot-database Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workf…

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uspto-database Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, …

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alphafold-database Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, …

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arboreto Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use wh…

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arxiv-search Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic …

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benchling-integration Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build…

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biomni Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecu…

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biorxiv-database Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints…

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biorxiv-search Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.

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bioservices Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL,…

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brenda-database Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data…

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cellxgene-census Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases,…

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cobrapy Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biolog…

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cosmic-database Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusi…

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dask Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy co…

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deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), …

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dnanexus-integration DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, …

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egocentric_view_to_structured_log Converts first-person XR headset video into a structured experiment timeline log. Extracts timestamped events (action…

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egohos-segmentation Egocentric Hand-Object Segmentation (EgoHOS) - pixel-level hand and object segmentation in egocentric videos. Outputs…

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ena-database Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by a…

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ensembl-database Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparat…

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etetoolkit Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NC…

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extract_experiment_data_from_video General-purpose experimental data extractor from lab video streams. Ingests footage from XR headsets or fixed cameras…

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flowio Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert t…

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gene-database Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenot…

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