Curated, auto-synced collection of 2,000+ Claude Code & Codex skills for AI4Protein, bioinformatics, AI development, and academic paper writing. One curl command installs them all.
Skill Claude Code
An AI-based health analysis system that combines health data from multiple sources to find unusual patterns, assess health risks, answer questions, and create health reports.
Skill Claude CodeCodex
Use after generating code, after accepting AI suggestions, or when reviewing AI-written modules. Also use when code works but feels brittle, when error handling seems thin, when orphaned resources or missing cleanup are suspected, or when the agent claims done but hidden debt may exist. Catches the specific failure…
Skill Claude CodeCodex
Engineering operating model for teams where AI agents generate a large share of implementation output.
Skill Claude CodeCodex
Regression testing strategies for AI-assisted development. Sandbox-mode API testing without database dependencies, automated bug-check workflows, and patterns to catch AI blind spots where the same model writes and reviews code.
Skill Codex
Eliminates AI-generated writing patterns that erode reader trust. Use when writing or editing articles, docs, or press releases.
Skill Claude CodeCodex
Build production Apache Airflow DAGs with best practices for operators, sensors, testing, and deployment. Use when creating data pipelines, orchestrating workflows, or scheduling batch jobs.
Skill Claude CodeCodex
AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. Monte Carlo tree search guided by a template-based neural expansion policy recursively disconnects a target SMILES until precursors are found in a purchasable stock. Covers config.yml (v4 format), aizynthcli batch screening, the…
Skill Claude CodeCodex
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright…
Skill Claude CodeCodex
Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
Skill Claude CodeCodex
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
Skill Claude CodeCodex
Quantify transcript expression from FASTQ with Salmon (selective alignment) or kallisto (pseudoalignment), bypassing genome mapping. Use when quantifying RNA-seq without alignment, deciding whether a decoy-aware index is required, detecting and verifying library strandedness, enabling GC and sequence bias correction…
Skill Claude CodeCodex
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Skill Claude CodeCodex
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
Skill Claude CodeCodex
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Skill Claude CodeCodex
Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
Skill Claude CodeCodex
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
Skill Claude CodeCodex
Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or…
Skill Claude CodeCodex
Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized…
Skill Claude CodeCodex
Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor…
Skill Claude CodeCodex
Access real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API. Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market…
Skill Claude CodeCodex
Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
Skill Claude CodeCodex
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
Skill Claude CodeCodex
Retrieves and interprets AlphaFold Protein Structure Database (AFDB) models by UniProt accession, reading pLDDT and PAE confidence correctly. Use when treating pLDDT as PER-RESIDUE confidence (not global accuracy) and recognizing a long low-pLDDT stretch as an intrinsically disordered region rather than a modeling…
Skill Claude CodeCodex
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: