# Skills for Science and research Skills for Science and research: what each one does, an install command and example prompts. 728 cards · page 5 of 19 - HTML: https://affpapa.org/en/nevibecode/skills/topic/science?page=5 - Instructions for agents: https://affpapa.org/en/nevibecode/agents.md - [typst-author](https://affpapa.org/en/nevibecode/skills/typst-author.md) — skill · jihe520 · Claude Code, Codex, Cursor +3 · 1800 installs — Generates, edits, and troubleshoots Typst markup while enforcing syntax rules and formatting checks. - [hugging-science](https://affpapa.org/en/nevibecode/skills/hugging-science.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1800 installs — A skill to find and evaluate scientific datasets, models, and interactive demos via the Hugging Science catalog. - [ginkgo-cloud-lab](https://affpapa.org/en/nevibecode/skills/ginkgo-cloud-lab.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Assists with protocol selection, input files, pricing checks, and orders for Ginkgo Bioworks Cloud Lab. - [primekg](https://affpapa.org/en/nevibecode/skills/primekg.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1900 installs — Wraps the PrimeKG precision-medicine CSV in pandas helpers, so the agent can look up typed nodes, neighbours, disease summaries and short paths without leaving the repo. - [glycoengineering](https://affpapa.org/en/nevibecode/skills/glycoengineering.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1800 installs — A skill for working through N- and O-glycosylation sites in protein sequences: motif scanning, mutation planning and predictor prep. - [mathmodel-figure-templates](https://affpapa.org/en/nevibecode/skills/mathmodel-figure-templates.md) — skill · jihe520 · Claude Code, Codex, Cursor +3 · 1700 installs — Runs packaged Python and matplotlib scripts to generate publication-grade scientific figures. - [exa-search](https://affpapa.org/en/nevibecode/skills/k-dense-ai-exa-search.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1700 installs — Skill for searching scientific and technical content via Exa with text extraction from pages and PDFs in batches. - [autoskill](https://affpapa.org/en/nevibecode/skills/autoskill.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1700 installs — Analyzes Screenpipe activity windows to detect repeating research workflows and drafts new skills for review. - [paper-spine](https://affpapa.org/en/nevibecode/skills/paper-spine.md) — skill · WUBING2023 · Claude Code, Codex, Cursor +3 · 1200 installs — Orchestrates academic paper drafting with evidence-bound citations, interactive web intake, and full in-task revisions. - [tavily-research](https://affpapa.org/en/nevibecode/skills/tavily-research.md) — skill · tavily-ai · Claude Code, Codex, Cursor +3 · 22000 installs — Runs deep web research via the Tavily CLI and returns a structured report with source citations. - [nextflow](https://affpapa.org/en/nevibecode/skills/nextflow.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1400 installs — Guides your AI agent in writing, running, and debugging Nextflow DSL2 pipelines and nf-core workflows on HPC or cloud runners. - [pathway-enrichment](https://affpapa.org/en/nevibecode/skills/pathway-enrichment.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1400 installs — Runs pathway and gene-set enrichment analysis on gene lists or ranked data, finds over-represented GO terms, KEGG, Reactome, MSigDB. - [experimental-design](https://affpapa.org/en/nevibecode/skills/experimental-design.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1400 installs — Helps you plan an experiment before collecting data: pick a design, randomize, block nuisance variation and lay out factor combinations. - [bulk-rnaseq](https://affpapa.org/en/nevibecode/skills/bulk-rnaseq.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1400 installs — Prepares bulk RNA-seq reads, Salmon, and STAR outputs into validated gene-level count matrices for differential expression in PyDESeq2. - [liteparse](https://affpapa.org/en/nevibecode/skills/k-dense-ai-liteparse.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1400 installs — Local document parser that returns text with bounding boxes. - [pacsomatic](https://affpapa.org/en/nevibecode/skills/pacsomatic.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1400 installs — Prepares a matched tumor-normal run of nf-core/pacsomatic on PacBio HiFi data: builds the samplesheet, writes launch artifacts, submits the Nextflow driver to a scheduler. - [statistical-power](https://affpapa.org/en/nevibecode/skills/statistical-power.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1300 installs — Calculates how many observations your study needs to reliably detect a meaningful effect. - [huggingface-papers](https://affpapa.org/en/nevibecode/skills/huggingface-papers.md) — skill · huggingface · Claude Code, Codex, Cursor +3 · 2200 installs — Pulls the paper ID out of a Hugging Face or arXiv link, reads the page as markdown, and fetches authors, models and datasets from the papers API. - [deep-research](https://affpapa.org/en/nevibecode/skills/ruvnet-deep-research.md) — skill · ruvnet · Claude Code, Codex, Cursor +3 · 893 installs — Orchestrates multi-phase research using web search, codebase analysis, and memory storage. - [arbor](https://affpapa.org/en/nevibecode/skills/arbor.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1200 installs — Runs an autonomous optimization loop using hypothesis trees for models, code, and harnesses. - [onekgpd](https://affpapa.org/en/nevibecode/skills/onekgpd.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1100 installs — Queries the 1000 Genomes Project cohort at the participant level. - [tamarind](https://affpapa.org/en/nevibecode/skills/tamarind.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 1100 installs — Runs Tamarind Bio structural biology and molecular design tools through its REST API or MCP server. - [ml-paper-writing](https://affpapa.org/en/nevibecode/skills/ml-paper-writing.md) — skill · Orchestra Research · Claude Code, Codex, Cursor +3 · 2300 installs — Guides ML and AI paper drafting from a research repository, with literature checks and preparation for conference submissions. - [research-synthesize](https://affpapa.org/en/nevibecode/skills/research-synthesize.md) — skill · ruvnet · Claude Code, Codex, Cursor +3 · 751 installs — Turns findings stored in ruflo memory into one report, with evidence grades, contradiction handling and next steps. - [mermaid-to-proverif](https://affpapa.org/en/nevibecode/skills/mermaid-to-proverif.md) — skill · trailofbits · Claude Code, Codex, Cursor +3 · 3900 installs — Turns a Mermaid sequence diagram of a crypto protocol into a ProVerif model — a .pv file you can check for secrecy, authentication and forward secrecy. - [huggingface-paper-publisher](https://affpapa.org/en/nevibecode/skills/huggingface-paper-publisher.md) — skill · huggingface · Claude Code, Codex, Cursor +3 · 1700 installs — Indexes arXiv papers on Hugging Face Hub, links them to model and dataset cards, verifies authorship and builds markdown drafts from templates. - [uncertainty-and-units](https://affpapa.org/en/nevibecode/skills/uncertainty-and-units.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 985 installs — Keeps physical units attached through a calculation and carries measurement uncertainty with pint and uncertainties, then checks that the answer is physically plausible. - [analytical-method-validation](https://affpapa.org/en/nevibecode/skills/analytical-method-validation.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 970 installs — Plans validation, verification and transfer work for analytical procedures under ICH, USP, CLSI and ISO frameworks. - [genomic-intelligence](https://affpapa.org/en/nevibecode/skills/genomic-intelligence.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 939 installs — A skill that runs six DNA sequence tasks on Genomic Intelligence's hosted models: promoters, splice sites, enhancers, chromatin, expression and gene annotation. - [genomic-coordinates](https://affpapa.org/en/nevibecode/skills/genomic-coordinates.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 950 installs — Converts genomic coordinates between BED, VCF, and GTF formats, and normalises variant representations. - [paperclip](https://affpapa.org/en/nevibecode/skills/k-dense-ai-paperclip.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 951 installs — Wires the GXL Paperclip CLI and Python SDK into your agent so it can search PMC papers, FDA documents and clinical trials, then cite exact lines. - [iso-standards-readiness](https://affpapa.org/en/nevibecode/skills/iso-standards-readiness.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 950 installs — Organizes evidence for ISO 13485, ISO 14971, ISO/IEC 17025, and ISO 15189 standards. - [ontology-term-resolution](https://affpapa.org/en/nevibecode/skills/ontology-term-resolution.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 948 installs — Resolves free-text scientific labels to ontology term IDs and validates CURIEs via EBI OLS4. - [openpiv](https://affpapa.org/en/nevibecode/skills/openpiv.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 943 installs — Skill for measuring fluid velocity fields from particle image pairs. - [pathogen-variant-surveillance](https://affpapa.org/en/nevibecode/skills/pathogen-variant-surveillance.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 936 installs — Queries public LAPIS data for pathogen variant surveillance, lineage checks, weekly sequence proportions, and reporting delays. - [pkpd-modeling](https://affpapa.org/en/nevibecode/skills/pkpd-modeling.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 935 installs — Runs non-compartmental and compartmental PK/PD calculations on concentration-time data, then spells out what the numbers assume. - [firecrawl-deep-research](https://affpapa.org/en/nevibecode/skills/firecrawl-deep-research.md) — skill · firecrawl · Claude Code, Codex, Cursor +3 · 35400 installs — Turns a hard topic into a cited analytical report: it gathers sources from the open web with Firecrawl, works several angles and links the evidence. - [firecrawl-research-papers](https://affpapa.org/en/nevibecode/skills/firecrawl-research-papers.md) — skill · firecrawl · Claude Code, Codex, Cursor +3 · 33800 installs — Discovers and synthesizes academic literature using Firecrawl Research. - [deepspot-m](https://affpapa.org/en/nevibecode/skills/deepspot-m.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 877 installs — Reads a 224x224 H&E tile and returns predicted log1p-CPM expression for the genes you ask about. - [relsa-severity-assessment](https://affpapa.org/en/nevibecode/skills/relsa-severity-assessment.md) — skill · K-Dense-AI · Claude Code, Codex, Cursor +3 · 874 installs — Calculates multivariate RELSA severity scores and ARIMA-based score forecasts for animal studies. Next: https://affpapa.org/en/nevibecode/skills/topic/science.md?page=6 ## Refine [research](https://affpapa.org/en/nevibecode/tag/research.md) · [python](https://affpapa.org/en/nevibecode/tag/python.md) · [bioinformatics](https://affpapa.org/en/nevibecode/tag/bioinformatics.md) · [genomics](https://affpapa.org/en/nevibecode/tag/genomics.md) · [latex](https://affpapa.org/en/nevibecode/tag/latex.md) · [citations](https://affpapa.org/en/nevibecode/tag/citations.md) · [arxiv](https://affpapa.org/en/nevibecode/tag/arxiv.md) · [pdf](https://affpapa.org/en/nevibecode/tag/pdf.md) · [machine-learning](https://affpapa.org/en/nevibecode/tag/machine-learning.md) · [api](https://affpapa.org/en/nevibecode/tag/api.md) · [statistics](https://affpapa.org/en/nevibecode/tag/statistics.md) · [markdown](https://affpapa.org/en/nevibecode/tag/markdown.md) ## Narrow this list Parameters: `?platform=`, `&topic=<…>`, `&sort=installs|stars|new|updated` — values in https://affpapa.org/en/nevibecode/agents.md --- NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md