Research & Search Agent Skills
Research agent skills teach AI agents to gather and synthesize information properly: literature reviews, competitive analysis, web research with citations, and structured summaries. Each SKILL.md encodes a method, not just a prompt, so results stay consistent across runs.
Research & Search
928 skills
k-dense-ai adaptyv
Submit protein sequences to the Adaptyv Bio Foundry for experimental characterization (binding, thermostability, expression, fluorescence) and retrieve results via API or Python SDK.
30.2k · bundle
k-dense-ai cobrapy
Perform constraint-based metabolic modeling with COBRApy: run FBA, FVA, gene knockouts, flux sampling, and manage SBML models for systems biology and metabolic engineering.
30.2k · bundle
k-dense-ai datamol
Simplify molecular cheminformatics with a Pythonic wrapper around RDKit for SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, and parallel processing.
30.2k · bundle
k-dense-ai lamindb
Manage biological datasets and models with LaminDB, an open-source lineage-native lakehouse. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation, collections, branches, storage, and workflow integrations.
30.2k · bundle
k-dense-ai matchms
Process and analyze mass spectrometry data: import spectra from MGF, mzML, MSP, and JSON formats; apply 40+ filters for metadata harmonization and peak cleaning; compute spectral similarities (cosine, modified cosine) for compound identification; build reproducible processing pipelines.
30.2k · bundle
k-dense-ai onekgpd
Query the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.
30.2k · bundle
k-dense-ai primekg
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
30.2k · bundle
k-dense-ai diffdock
Predict 3D binding poses of small molecule ligands to protein targets using diffusion-based molecular docking, supporting single complexes, batch processing, and virtual screening.
30.2k · bundle
k-dense-ai fluidsim
Run computational fluid dynamics simulations using Python, including Navier-Stokes equations, shallow water, and stratified flows with pseudospectral methods and HPC support.
30.2k · bundle
k-dense-ai networkx
Create, analyze, and visualize complex networks and graphs in Python with NetworkX, including graph algorithms, community detection, synthetic network generation, and multiple I/O formats.
30.2k · bundle
k-dense-ai pydeseq2
Perform differential gene expression analysis for bulk RNA-seq data using PyDESeq2, supporting formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.
30.2k · bundle
k-dense-ai pymatgen
Analyze and manipulate crystal structures, compute phase diagrams, and access the Materials Project database using the pymatgen library.
30.2k · bundle
k-dense-ai pyopenms
Analyze proteomics and metabolomics mass spectrometry data with PyOpenMS: read/write MS file formats, process spectra, detect and quantify features, identify peptides and proteins, and run end-to-end LC-MS/MS pipelines using ready-to-run scripts.
30.2k · bundle
k-dense-ai pyzotero
Manage Zotero reference libraries programmatically using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3.
30.2k · bundle
k-dense-ai tamarind
Run computational biology tools for protein structure prediction, design, docking, and molecular dynamics on managed cloud GPUs via REST API or MCP server.
30.2k · bundle
k-dense-ai biopython
Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.
30.2k · bundle
k-dense-ai deeptools
Process and analyze high-throughput sequencing data with deepTools for quality control, normalization, comparison, and publication-quality visualizations of ChIP-seq, RNA-seq, and ATAC-seq experiments.
30.2k · bundle
k-dense-ai hypogenic
Automates hypothesis generation and testing on tabular datasets using LLMs, combining data-driven discovery with literature integration for scientific research.
30.2k · bundle
k-dense-ai neurokit2
Process and analyze physiological signals including ECG, EEG, EDA, RSP, PPG, EMG, and EOG using Python.
30.2k · bundle
k-dense-ai pennylane
Train quantum circuits like neural networks with automatic differentiation, device-independent programming, and integration with PyTorch or JAX.
30.2k · bundle
k-dense-ai tiledbvcf
Store, query, and export genomic variant data (VCF/BCF) using TileDB's sparse array technology for scalable population genomics workflows.
30.2k
k-dense-ai torchdrug
Build and train graph neural networks for drug discovery, protein modeling, and molecular science using PyTorch-native tools.
30.2k · bundle
k-dense-ai etetoolkit
Manipulate phylogenetic trees, detect evolutionary events, integrate NCBI taxonomy, and create publication-quality visualizations using the ETE toolkit.
30.2k · bundle
k-dense-ai exa-search
Search the web and extract content from URLs using Exa, with support for academic and scientific sources.
30.2k · bundle
k-dense-ai paperzilla
Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Fetch feeds, read papers, leave feedback, and export data using the pz CLI.
30.2k
k-dense-ai pylabrobot
Control liquid handling robots, plate readers, pumps, and other lab equipment through a unified Python interface across platforms.
30.2k · bundle
k-dense-ai scikit-bio
Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.
30.2k · bundle
k-dense-ai bioservices
Query 40+ bioinformatics services (UniProt, KEGG, ChEMBL, Reactome) with a unified Python interface for cross-database analysis, identifier mapping, and sequence analysis.
30.2k · bundle
k-dense-ai bulk-rnaseq
Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.
30.2k · bundle
k-dense-ai peer-review
Evaluate scientific manuscripts and grant proposals with structured, checklist-based peer review covering methodology, statistics, reproducibility, ethics, and reporting standards.
30.2k · bundle
k-dense-ai infographics
Generate publication-quality infographics using Nano Banana Pro AI with Gemini 3 Pro quality review and optional Perplexity Sonar research. Supports 10 infographic types, 8 industry styles, and colorblind-safe palettes.
30.2k · bundle
k-dense-ai paper-lookup
Search 10 academic literature APIs for papers, preprints, citations, and open-access full text with reproducible provenance.
30.2k · bundle
k-dense-ai parallel-web
Search the web, extract URL content, enrich datasets with web-sourced fields, and run deep research reports, prioritizing academic and scientific sources.
30.2k · bundle
k-dense-ai open-notebook
Self-host an open-source research notebook with AI-powered note generation, multi-speaker podcast creation, and context-aware document chat, supporting 16+ AI providers.
30.2k · bundle
k-dense-ai phylogenetics
Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.
30.2k · bundle
k-dense-ai dhdna-profiler
Analyze any text to extract a cognitive fingerprint across 12 dimensions, revealing reasoning patterns, decision styles, and thinking signatures.
30.2k · bundle
Frequently asked questions
What are Research & Search agent skills?
Research agent skills teach AI agents to gather and synthesize information properly: literature reviews, competitive analysis, web research with citations, and structured summaries. Each SKILL.md encodes a method, not just a prompt, so results stay consistent across runs.
Which Research & Search skills are most installed?
Popular Research & Search skills on SkillMD right now include open-notebook, primekg, fluidsim. Rankings shift as installs change; sort this page by "Most downloaded" for the live list.
Do Research & Search skills work with Claude Code and Cursor?
Yes. Every skill here ships as a SKILL.md file, an open format that works in Claude Code, Claude.ai, Cursor, Codex, Windsurf, and 60+ other agents. Install one with npx skillmds add <owner>/<name>, or copy the file into your agent's skills directory.