Directory / Category / Science, research & learning

Science, research & learning: agent skills and plugins

192 entries: 5 from Claude Code, 1 from Anthropic skills, 5 from Codex, 177 from K-Dense science, 4 from Awesome Copilot. Categories are our keyword-based grouping (see methodology); each entry also keeps its catalog's own category where one exists.

Software development Deployment, cloud & DevOps Data & databases Security Design & media Documents & office files Productivity & business Other

192 of 192 shown. Click a column header to sort.


math-proof Two skills for hard mathematics problems, each ending in a self-contained proof.md: /math-proof:solo has the session work the problem itself in stages…	Claude Code	plugin	Science, research & learning	43,046	2026-09-30	Anthropic	see LICENSE file
Consensus Consensus is the go-to MCP for academic research. Connect directly to 220M+ peer-reviewed papers to search, synthesize, and build structured research …	Codex	plugin	Science, research & learning	7,502	2026-08-27	Consensus	–
academy-guide Stop and check this skill before finishing any reply to a question about how to use Claude or a Claude product — it recommends matching courses, tutor…	Anthropic skills	skill	Science, research & learning	182,130	2026-08-18	Anthropic	Complete terms in LICENSE.txt
Boltz Predict structures, screen molecules and proteins, and design binders.	Codex	plugin	Science, research & learning	7,502	2026-06-22	Boltz	MIT
learn-with-coursera Turn any learning intent into a personalized Coursera experience. Asks three quick questions (topic, familiarity, preferred format), searches Coursera…	Claude Code	plugin	Science, research & learning	1	2026-06-19	Coursera	–
Life Sciences NGS Analysis Guided NGS intake, local execution, and public-pipeline routing for BCL, FASTQ, DNA variant, RNA-seq, single-cell, epigenomics, amplicon, and metageno…	Codex	plugin	Science, research & learning	7,502	2026-06-03	OpenAI	MIT
Zotero Work with Zotero from Codex: search your library, export BibTeX, insert citations, and import references through the Zotero desktop app.	Codex	plugin	Science, research & learning	7,502	2026-05-04	OpenAI	MIT
Life Science Research General life-sciences research workflows with query routing, evidence synthesis, and optional parallel subagent analysis across genetics, omics, biolo…	Codex	plugin	Science, research & learning	7,502	2026-04-09	OpenAI	Proprietary
math-olympiad Solve competition math (IMO, Putnam, USAMO) with adversarial verification that catches what self-verification misses. Fresh-context verifiers attack p…	Claude Code	plugin	Science, research & learning	43,046	2026-03-30	Anthropic	see LICENSE file
13c-metabolic-flux Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation,…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
adaptyv Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory p…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
aeon This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, seg…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
alphagenome Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus r…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
analytical-method-validation Plans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
anndata Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—fo…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
arbor Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis a…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
arboreto Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
astropy Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time s…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
autoskill Analyzes user-requested Screenpipe history windows to detect repeated research workflows, match existing scientific skills, and stage new skill drafts…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
benchling-integration Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Us…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
bgpt-paper-search Searches BGPT scientific papers by topic or DOI and retrieves claim-level evidence extracted from full text, including experiments, reported statistic…	K-Dense science	skill	Science, research & learning	52,795	–	BGPT	MIT
bids Organizes, queries, validates, and converts Brain Imaging Data Structure (BIDS) datasets. Supports organizing neuroscience and biomedical data (MRI, E…	K-Dense science	skill	Science, research & learning	52,795	–	Yaroslav Halchenko	https://creativecommons.org/licenses/by/4.0/
biopython Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entr…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	Biopython License Agreement
bioservices Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protei…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	GPLv3
build-evidence-map Build an auditable evidence map for a contested technical choice, research synthesis, proposal review, or consequential decision. Use when Copilot mus…	Awesome Copilot	skill	Science, research & learning	40,178	–	–	MIT
bulk-rnaseq Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression. Covers nf-core/rnaseq and standalone quantif…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cantera Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cellprofiler Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/ch…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cellxgene-census Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cirq Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	Apache-2.0
citation-management Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate c…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
clinical-decision-support Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governanc…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
clinical-reports Creates safety-bounded draft structures and runs local deterministic checks for clinical case, diagnostic, trial, safety, and aggregate research repor…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
cobrapy Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	GPL-2.0
competitor-ad-intelligence Use this skill when the user asks to analyze, tear down, or reverse-engineer a competitor's paid ads. Trigger for prompts like "what ads is [competito…	Awesome Copilot	skill	Science, research & learning	40,178	–	GooseWorks	MIT
consciousness-council Structures a multi-perspective council exercise for decisions, research trade-offs, and creative challenges. Simulates thinking archetypes, separates …	K-Dense science	skill	Science, research & learning	52,795	–	AHK Strategies (ashrafkahoush-ux)	MIT
dask Scales pandas, NumPy, and custom Python research workflows beyond memory or across clusters with Dask. Covers DataFrames, Arrays, Bags, Futures, chunk…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
database-lookup Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a scientific, regulatory, financial, o…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
datalad Retrieves, versions, and publishes scientific datasets with DataLad and git-annex, and captures computational provenance with datalad run, rerun, and …	K-Dense science	skill	Science, research & learning	52,795	–	Dylan Pulver	MIT
datamol Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standar…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	Apache-2.0
deepchem Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked lab…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
deepspot-m Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Used for predicted log1p-CPM expression from 224x224 …	K-Dense science	skill	Science, research & learning	52,795	–	Ratschlab, ETH Zurich	PolyForm-Noncommercial-1.0.0
deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq v…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD
depmap Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers,…	K-Dense science	skill	Science, research & learning	52,795	–	Kuan-lin Huang	CC-BY-4.0
dhdna-profiler Applies the DHDNA framework as an exploratory rubric for reasoning and writing patterns in supplied text. Used for explicit requests for DHDNA, cognit…	K-Dense science	skill	Science, research & learning	52,795	–	AHK Strategies (ashrafkahoush-ux)	MIT
diffdock Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triag…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
dnanexus-integration Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Suppo…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
doc-and-modernize Two related workflows for a locally-cloned codebase, in one skill. Documentation mode produces a single, comprehensive, verifiable architecture docume…	Awesome Copilot	skill	Science, research & learning	40,178	–	–	MIT
esm Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohu…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
etetoolkit Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topolo…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	GPL-3.0-or-later
exa-search Searches scientific and technical web content with Exa and extracts page or PDF text from URLs in batches. Supports scholarly discovery with the publi…	K-Dense science	skill	Science, research & learning	52,795	–	Exa	MIT
experimental-design Designs experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
explanatory-output-style Adds educational insights about implementation choices and codebase patterns (mimics the deprecated Explanatory output style)	Claude Code	plugin	Science, research & learning	43,046	–	Anthropic	see LICENSE file
exploratory-data-analysis Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
fictiv Operates Fictiv (app.fictiv.com), the on-demand manufacturing platform, end to end in the user's browser. Covers uploading CAD parts, configuring proc…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
flowio Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, …	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	BSD-3-Clause
flowkit Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strat…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
fluidsim Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT
folklore-variant-evidence Retrieves ClinGen gene-disease validity assertions for a public gene or disease, and reviews source-linked public evidence and literature for one supp…	K-Dense science	skill	Science, research & learning	52,795	–	Helena Bioinformatics	MIT
generate-image Generates or edits images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrat…	K-Dense science	skill	Science, research & learning	52,795	–	K-Dense Inc.	MIT

Science, research & learning: agent skills and plugins

Get the new agent skills and plugins