scientific-skills

Plugin scientific-skills from marketplace claude-scientific-skills in Yezez9/Research-Agent. Commands read from the repo's manifest — 1 month ago.

Skills (174)

• adaptyv

  Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experi

• aeon

  This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorit

• alpha-vantage

  Access real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API. Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, option

• alphafold-database

  Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

• anndata

  Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

• arboreto

  Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed comp

• astropy

  Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use

• benchling-integration

  Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

• bgpt-paper-search

  Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimenta

• bindingdb-database

  Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.

• biopython

  Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integ

• biorxiv-database

  Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

• bioservices

  Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipu

• brenda-database

  Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

• cbioportal-database

  Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling.

• cellxgene-census

  Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.

• chembl-database

  Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

• cirq

  Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pe

• citation-management

  Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to Bi

• clinical-decision-support

  Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence

• clinical-reports

  Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP)

• clinicaltrials-database

  Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.

• clinpgx-database

  Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

• clinvar-database

  Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

• cobrapy

  Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

• consciousness-council

  Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a problem from multiple angles, requests devi

• cosmic-database

  Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

• dask

  Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; fo

• datacommons-client

  Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for queryi

• datamol

  Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or cu

• deepchem

  Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For

• deeptools

  NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

• denario

  Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches,

• depmap

  Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.

• dhdna-profiler

  Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my thinking style", "analyze how this person reas

• diffdock

  Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

• dnanexus-integration

  DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

• docx

  Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterhea

• drugbank-database

  Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-dr

• edgartools

  Python library for accessing, analyzing, and extracting data from SEC EDGAR filings. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly

• ena-database

  Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

• ensembl-database

  Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

• esm

  Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; desig

• etetoolkit

  Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

• exploratory-data-analysis

  Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown rep

• fda-database

  Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

• flowio

  Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

• fluidsim

  Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods

• fred-economic-data

  Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources. Access GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, and academic

• gene-database

  Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

• generate-image

  Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use th

• geniml

  This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to

• geo-database

  Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

• geomaster

  Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, poin

• geopandas

  Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving readi

• get-available-resources

  This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions s

• gget

  Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioser

• ginkgo-cloud-lab

  Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or optimization), generate fluorescent pixel art, or inte

• glycoengineering

  Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.

• gnomad-database

  Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.

• gtars

  High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

• gtex-database

  Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs. Essential for linking GWAS variants to gene regulation, understanding tissue-specific expression, and interpreting non-coding variant effects.

• gwas-database

  Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

• hedgefundmonitor

  Query the OFR (Office of Financial Research) Hedge Fund Monitor API for hedge fund data including SEC Form PF aggregated statistics, CFTC Traders in Financial Futures, FICC Sponsored Repo volumes, and FRB SCOOS dealer financing terms. Access time series data on hedge fund size, leverage, counterpart

• histolab

  Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning p

• hmdb-database

  Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

• hypogenic

  Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis f

• hypothesis-generation

  Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-br

• imaging-data-commons

  Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.

• infographics

  Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.

• interpro-database

  Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, and 11 other member databases. Use for protein function prediction, domain architecture analysis, evolutionary classification, and GO term mapping.

• iso-13485-certification

  Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required p

• jaspar-database

  Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class; scan DNA sequences for TF binding sites; compare matrices; essential for regulatory genomics, motif analysis, and GWAS regulatory variant interpretation.

• kegg-database

  Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

• labarchive-integration

  Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

• lamindb

  This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating dat

• latchbio-integration

  Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

• latex-posters

  Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for vis

• literature-review

  Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical,

• markdown-mermaid-writing

  Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templ

• market-research-reports
• markitdown
• matchms
• matlab
• matplotlib
• medchem
• metabolomics-workbench-database
• modal
• molecular-dynamics
• molfeat
• monarch-database
• networkx
• neurokit2
• neuropixels-analysis
• offer-k-dense-web
• omero-integration
• open-notebook
• openalex-database
• opentargets-database
• opentrons-integration
• paper-2-web
• parallel-web
• pathml
• pdb-database
• pdf
• peer-review
• pennylane
• perplexity-search
• phylogenetics
• plotly
• polars
• pptx-posters
• pptx
• primekg
• protocolsio-integration
• pubchem-database
• pubmed-database
• pufferlib
• pydeseq2
• pydicom
• pyhealth
• pylabrobot
• pymatgen
• pymc
• pymoo
• pyopenms
• pysam
• pytdc
• pytorch-lightning
• pyzotero
• qiskit
• qutip
• rdkit
• reactome-database
• research-grants
• research-lookup
• rowan
• scanpy
• scholar-evaluation
• scientific-brainstorming
• scientific-critical-thinking
• scientific-schematics
• scientific-slides
• scientific-visualization
• scientific-writing
• scikit-bio
• scikit-learn
• scikit-survival
• scvelo
• scvi-tools
• seaborn
• shap
• simpy
• stable-baselines3
• statistical-analysis
• statsmodels
• string-database
• sympy
• tiledbvcf
• timesfm-forecasting
• torch-geometric
• torchdrug
• transformers
• treatment-plans
• umap-learn
• uniprot-database
• usfiscaldata
• uspto-database
• vaex
• venue-templates
• what-if-oracle
• xlsx
• zarr-python
• zinc-database