Skill Claude CodeCodex
Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a…
Skill Claude CodeCodex
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene…
Skill Claude CodeCodex
Infers exact amplicon sequence variants (ASVs) from demultiplexed 16S rRNA or ITS amplicon FASTQ with DADA2 - removing primers with cutadapt (--discard-untrimmed), learning a per-run error model (filterAndTrim -> learnErrors -> dada -> mergePairs), merging run-level tables with mergeSequenceTables, then one…
Skill Claude CodeCodex
Profiles the antimicrobial-resistance gene content (resistome) of shotgun metagenomes - read-based quantification with RGI bwt, AMR++/MEGARes, ARGs-OAP/SARG, deepARG, or GROOT, and presence calling with AMRFinderPlus/ABRicate on assembled contigs or MAGs. Covers why an ARG hit is a sequence match not a phenotype, why…
Skill Claude CodeCodex
Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization…
Skill Claude Code
Plans, executes, and documents validation, verification, and transfer of analytical procedures under the governing framework - ICH Q2(R2) and Q14, USP / / , ICH M10 bioanalytical, CLSI EP, or ISO/IEC 17025. Use for HPLC, LC-MS/MS, GC, CE, ICP-MS, dissolution, qNMR, qPCR, NIR, and ligand binding or cell-based assays…
Skill Claude CodeCodex
Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (330 haploid copies/ng), the lambda = inputGE x VAF sampling ceiling (lambda>=3 for 95% detection), the error-suppression ladder (raw…
Skill Claude CodeCodex
Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when…
Skill Claude CodeCodex
Clean Architecture patterns for Android and Kotlin Multiplatform projects — module structure, dependency rules, UseCases, Repositories, and data layer patterns.
Skill Claude CodeCodex
Migrate from AngularJS to Angular using hybrid mode, incremental component rewriting, and dependency injection updates. Use when upgrading AngularJS applications, planning framework migrations, or modernizing legacy Angular code.
Skill Claude CodeCodex
Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (obsp/varp), uns. Use for .h5ad/.zarr I/O, concatenation, scverse integration. For analysis use scanpy; for probabilistic models use scvi-tools.
Skill Claude Code
Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
Skill Claude CodeCodex
Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution…
Skill Claude CodeCodex
Transfers gene annotations between genome assemblies via coordinate liftover (UCSC liftOver, CrossMap for same-species version updates) or feature/sequence projection (Liftoff for same/close species, miniprot for protein-level cross-species, TOGA/GeMoMa/CAT for distant clades). Covers the coordinate-vs-projection…
Skill Claude CodeCodex
Understand anti-reversing, obfuscation, and protection techniques encountered during software analysis. Use this skill when analyzing malware evasion techniques, when implementing anti-debugging protections for CTF challenges, when reverse engineering packed binaries, or when building security research tools that need…
Skill Claude Code
Skill "mage-antibody-generator" from FridrichMethod/awesome-skills, covering copyright notice, copyright (c) 2026 md babu mia, phd, all rights reserved, this code is proprietary and confidential and provenance: authenticated by md babu mia.
Skill Claude Code
An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).
Skill Claude CodeCodex
Master REST and GraphQL API design principles to build intuitive, scalable, and maintainable APIs that delight developers. Use when designing new APIs, reviewing API specifications, or establishing API design standards.
Skill Claude CodeCodex
REST API design patterns including resource naming, status codes, pagination, filtering, error responses, versioning, and rate limiting for production APIs.
Skill Codex
API hardening for Express, FastAPI, and serverless. Use for rate limiting, CORS, input validation, API keys, or OWASP API Top 10.
Skill Claude Code
Applies Arbor Hypothesis Tree Refinement to research artifacts with repeatable evaluators, including model training, agent harnesses, data synthesis and benchmark optimization. Uses persistent hypotheses, isolated experiments, evidence propagation and held-out candidate comparison for multi-experiment research runs.…
Skill Claude CodeCodex
GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest). Load matrix, filter by TFs, infer TF-target-importance links, save network. Dask-parallelized to single-cell scale. Core SCENIC component.
Skill Claude CodeCodex
Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3. Use for transcription factor-target association ranking, compatible Dask execution, sparse expression inputs, and network stability checks.
Skill Claude CodeCodex
Write and maintain Architecture Decision Records (ADRs) following best practices for technical decision documentation. Use when documenting significant technical decisions, reviewing past architectural choices, or establishing decision processes.
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: