yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my thinking style", "analyze how this person reasons", "cognitive…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Use when working directly with the esm Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional research-paper category and academic domain filtering) and URL extraction (fetching…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so the results will actually be interpretable. Use whenever someone is planning a study, asks how to assign subjects/samples to groups, mentions randomization, blocking…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or optimization), generate fluorescent pixel art, or interact with Ginkgo…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for simple pipelines, dataset preparation, and quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery, protein design, weather modeling, theorem proving, single-cell, or PDE solving. Hugging Science is a curated catalog…
yanjumlinnb-boop/scientific-agent-skills
Skill Claude CodeCodex
Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use…