Science and research: skills, plugins, subagents, slash commands and mcp servers

simpy K-Dense-AI skill Builds, tests, and inspects process-based discrete-event simulations using SimPy. Helpful for modeling service queues, logistics, and resource contention. Claude Code CX Codex Cursor +1 1,900installs geomaster K-Dense-AI skill Guides geospatial research work with satellite imagery, vector and raster GIS data, coordinate systems, spatial statistics, and Earth observation models. Claude Code CX Codex Cursor +1 1,900installs scikit-bio K-Dense-AI skill Analyzes biological sequences, alignments, and phylogenetic trees directly in your terminal. Helpful for microbiome workflows and ecology data. Claude Code CX Codex Cursor +1 1,900installs geopandas K-Dense-AI skill Guides Python geospatial workflows using GeoPandas, audits vector geometries, and verifies CRS transformations before execution. Claude Code CX Codex Cursor +1 1,900installs research-lookup K-Dense-AI skill Collects verified academic articles and references for a manuscript or review when you need 60+ sources. Uses parallel search, extracts data from PDFs and web sources, supports deep exhaustive search and optional Perplexity. Claude Code CX Codex Cursor +1 1,900installs biopython K-Dense-AI skill Automates computational biology workflows: parses sequence files, runs alignments, and fetches records via NCBI Entrez. Claude Code CX Codex Cursor +1 1,900installs torch-geometric K-Dense-AI skill Guides work with PyTorch Geometric graph neural networks, from graph data setup to classification tasks. Use it when a project relies on torch_geometric. Claude Code CX Codex Cursor +1 1,900installs venue-templates K-Dense-AI skill Prepares journal manuscripts, conference papers, research posters, and grant documents with current venue rules and bundled LaTeX scaffolds. Verifies page limits, anonymity requirements, and formatting before submission. Claude Code CX Codex Cursor +1 1,900installs open-notebook K-Dense-AI skill Organizes research notes, citations, and document chat using self-hosted storage and AI providers. Helpful for managing an Open Notebook setup directly from your agent. Claude Code CX Codex Cursor +1 1,900installs sr-screener Imbad0202 skill Applies protocol-driven screening to study records for reviews. It manages double-blind screening of titles, abstracts, and full texts. Claude Code CX Codex Cursor +1 449installs typst-author jihe520 skill Generates, edits, and troubleshoots Typst markup while enforcing syntax rules and formatting checks. Keeps agents grounded against hallucinations. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +1 1,800installs 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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +1 1,700installs paper-spine WUBING2023 skill Orchestrates academic paper drafting with evidence-bound citations, interactive web intake, and full in-task revisions. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +1 21,900installs 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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +1 1,700installs 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. Claude Code CX Codex Cursor +1 939installs 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. Claude Code CX Codex Cursor +1 937installs 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. Claude Code CX Codex Cursor +1 924installs firecrawl-research-papers firecrawl skill Discovers and synthesizes academic literature using Firecrawl Research. Builds structured reviews from PubMed, bioRxiv, medRxiv, and arXiv papers. Claude Code CX Codex Cursor +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. Claude Code CX Codex Cursor +1 866installs 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. Claude Code CX Codex Cursor +1 863installs manimce-best-practices adithya-s-k skill A skill that steers the agent through Manim Community Edition: scenes, MathTex, 3D, camera work. Useful once a project starts with from manim import *. Claude Code CX Codex Cursor +1 3,900installs