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NeVibeCode · 676 items

Skills for Science and research

Skills for Science and research: what each one does, an install command and example prompts.

typst-author jihe520 skill Generates, edits, and troubleshoots Typst markup while enforcing syntax rules and formatting checks. Keeps agents grounded against hallucinations. CX Codex +1 1,800installs hugging-science K-Dense-AI skill A skill to find and evaluate scientific datasets, models, and interactive demos via the Hugging Science catalog. Use it when you need an ML resource for biology, chemistry, genomics, materials science, climate, or physics. CX Codex +1 1,800installs ginkgo-cloud-lab K-Dense-AI skill Assists with protocol selection, input files, pricing checks, and orders for Ginkgo Bioworks Cloud Lab. Useful for RNA synthesis and automated protein expression. CX Codex +1 1,900installs primekg K-Dense-AI skill 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. CX Codex +1 1,900installs glycoengineering K-Dense-AI skill A skill for working through N- and O-glycosylation sites in protein sequences: motif scanning, mutation planning and predictor prep. CX Codex +1 1,800installs mathmodel-figure-templates jihe520 skill Runs packaged Python and matplotlib scripts to generate publication-grade scientific figures. Useful when you need Taylor diagrams, ROC curves, or correlation grids quickly. CX Codex +1 1,700installs exa-search K-Dense-AI skill Skill for searching scientific and technical content via Exa with text extraction from pages and PDFs in batches. Supports filtering by publication category and academic domains. CX Codex +1 1,700installs autoskill K-Dense-AI skill Analyzes Screenpipe activity windows to detect repeating research workflows and drafts new skills for review. Runs strictly on explicit user demand. CX Codex +1 1,700installs paper-spine WUBING2023 skill Orchestrates academic paper drafting with evidence-bound citations, interactive web intake, and full in-task revisions. CX Codex +1 1,200installs tavily-research tavily-ai skill Runs deep web research via the Tavily CLI and returns a structured report with source citations. Useful for market reviews and multi-source technical comparisons. CX Codex +1 22,000installs nextflow K-Dense-AI skill Guides your AI agent in writing, running, and debugging Nextflow DSL2 pipelines and nf-core workflows on HPC or cloud runners. CX Codex +1 1,400installs pathway-enrichment K-Dense-AI skill Runs pathway and gene-set enrichment analysis on gene lists or ranked data, finds over-represented GO terms, KEGG, Reactome, MSigDB. Needed after differential expression, CRISPR screens, or clustering. CX Codex +1 1,400installs experimental-design K-Dense-AI skill Helps you plan an experiment before collecting data: pick a design, randomize, block nuisance variation and lay out factor combinations. Useful while the study is still on paper. CX Codex +1 1,400installs bulk-rnaseq K-Dense-AI skill Prepares bulk RNA-seq reads, Salmon, and STAR outputs into validated gene-level count matrices for differential expression in PyDESeq2. CX Codex +1 1,400installs liteparse K-Dense-AI skill Local document parser that returns text with bounding boxes. Use it for layout-aware RAG, OCR on scanned papers, and batch ingestion of research folders. CX Codex +1 1,400installs pacsomatic K-Dense-AI skill 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. CX Codex +1 1,400installs statistical-power K-Dense-AI skill Calculates how many observations your study needs to reliably detect a meaningful effect. Supports protocol planning, grant submissions, and pre-registration — from basic t-tests to complex mixed models and survival analysis. CX Codex +1 1,300installs huggingface-papers huggingface skill 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. CX Codex +1 2,200installs deep-research ruvnet skill Orchestrates multi-phase research using web search, codebase analysis, and memory storage. It generates structured findings with evidence ratings for complex topics. CX Codex +1 893installs arbor K-Dense-AI skill Runs an autonomous optimization loop using hypothesis trees for models, code, and harnesses. Useful when organizing dozens of experimental trials without losing past findings. CX Codex +1 1,200installs onekgpd K-Dense-AI skill Queries the 1000 Genomes Project cohort at the participant level. It identifies variant carriers across 3,202 individuals and calculates relatedness. CX Codex +1 1,100installs tamarind K-Dense-AI skill Runs Tamarind Bio structural biology and molecular design tools through its REST API or MCP server. Use it for cloud jobs without local GPUs. CX Codex +1 1,100installs ml-paper-writing Orchestra Research skill Guides ML and AI paper drafting from a research repository, with literature checks and preparation for conference submissions. CX Codex +1 2,300installs research-synthesize ruvnet skill Turns findings stored in ruflo memory into one report, with evidence grades, contradiction handling and next steps. Useful after a run of deep-research. CX Codex +1 751installs mermaid-to-proverif trailofbits skill 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. CX Codex +1 3,900installs huggingface-paper-publisher huggingface skill Indexes arXiv papers on Hugging Face Hub, links them to model and dataset cards, verifies authorship and builds markdown drafts from templates. CX Codex +1 1,700installs uncertainty-and-units K-Dense-AI skill Keeps physical units attached through a calculation and carries measurement uncertainty with pint and uncertainties, then checks that the answer is physically plausible. CX Codex +1 985installs analytical-method-validation K-Dense-AI skill Plans validation, verification and transfer work for analytical procedures under ICH, USP, CLSI and ISO frameworks. Use it to assess whether a method suits its intended purpose. CX Codex +1 970installs genomic-intelligence K-Dense-AI skill A skill that runs six DNA sequence tasks on Genomic Intelligence's hosted models: promoters, splice sites, enhancers, chromatin, expression and gene annotation. No local GPU. CX Codex +1 939installs genomic-coordinates K-Dense-AI skill Converts genomic coordinates between BED, VCF, and GTF formats, and normalises variant representations. Useful when reconciling coordinate systems, indels, and assembly contigs. CX Codex +1 950installs paperclip K-Dense-AI skill 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. CX Codex +1 951installs iso-standards-readiness K-Dense-AI skill Organizes evidence for ISO 13485, ISO 14971, ISO/IEC 17025, and ISO 15189 standards. Structures controlled documents, risk files, and traceability records for human review. CX Codex +1 950installs ontology-term-resolution K-Dense-AI skill Resolves free-text scientific labels to ontology term IDs and validates CURIEs via EBI OLS4. Useful for preparing dataset metadata for GEO, BioSamples, or CELLxGENE. CX Codex +1 948installs openpiv K-Dense-AI skill Skill for measuring fluid velocity fields from particle image pairs. Handles window cross-correlation, vector validation, vorticity and turbulence calculation — built for experimental flow visualization analysis. CX Codex +1 943installs pathogen-variant-surveillance K-Dense-AI skill Queries public LAPIS data for pathogen variant surveillance, lineage checks, weekly sequence proportions, and reporting delays. CX Codex +1 936installs pkpd-modeling K-Dense-AI skill Runs non-compartmental and compartmental PK/PD calculations on concentration-time data, then spells out what the numbers assume. CX Codex +1 935installs firecrawl-deep-research firecrawl skill 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. CX Codex +1 35,400installs firecrawl-research-papers firecrawl skill Discovers and synthesizes academic literature using Firecrawl Research. Builds structured reviews from PubMed, bioRxiv, medRxiv, and arXiv papers. CX Codex +1 33,800installs deepspot-m K-Dense-AI skill Reads a 224x224 H&E tile and returns predicted log1p-CPM expression for the genes you ask about. Useful when you want spatial transcriptomics from a slide you have already scanned. CX Codex +1 877installs relsa-severity-assessment K-Dense-AI skill Calculates multivariate RELSA severity scores and ARIMA-based score forecasts for animal studies. Useful for 3Rs reporting and EU Directive 2010/63/EU compliance. CX Codex +1 874installs

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