peer-review
145Skill Claude CodeCodex
Conduct thorough academic peer reviews with structured feedback using loadpdf and arxivtoprompt.
not rated 60 5mo ago A 19 tokens
original MIT
60Stars on the repository
200Mods indexed here, across every type
5mo agoLast push, which is what freshness is scored on
MITLicence, which decides whether bodies are shown
quant-analysis
146Skill Claude CodeCodex
Quantitative finance analysis including portfolio optimization, risk modeling, and time series econometrics using jupyterexecute.
not rated 60 5mo ago A 23 tokens
original MIT
theorem-proving
147Skill Claude CodeCodex
Construct and verify mathematical proofs using LaTeX typesetting and computational verification via jupyterexecute.
not rated 60 5mo ago A 23 tokens
original MIT
protocol-writing
148Skill Claude CodeCodex
Write clear, reproducible experimental protocols and Standard Operating Procedures (SOPs) for any scientific discipline.
not rated 60 5mo ago A 0 tokens
copy · 91% MIT
Skill Claude CodeCodex
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io…
not rated 60 5mo ago B 85 tokens
copy · 95% MIT
pubchem-database
150Skill Claude CodeCodex
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
not rated 60 5mo ago A 49 tokens
copy · 86% MIT
pubmed-database
151Skill Claude CodeCodex
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
not rated 60 5mo ago A 58 tokens
copy · 84% MIT
pubmed-search
152Skill Claude CodeCodex
Search PubMed biomedical literature with natural language queries powered by Valyu semantic search. Full-text access, integrate into your AI projects.
not rated 60 5mo ago B 30 tokens
copy · 86% MIT
pufferlib
153Skill Claude CodeCodex
High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or…
not rated 60 5mo ago A 78 tokens
copy · 89% MIT
pydeseq2
154Skill Claude CodeCodex needs its repo
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
not rated 60 5mo ago A 45 tokens
copy · 95% MIT
pydicom
155Skill Claude CodeCodex needs its repo
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags…
not rated 60 5mo ago A 110 tokens
copy · 80% MIT
pyhealth
156Skill Claude CodeCodex
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC)…
not rated 60 5mo ago A 109 tokens
copy · 88% MIT
pylabrobot
157Skill Claude CodeCodex
Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API…
not rated 60 5mo ago A 73 tokens
copy · 97% MIT
pymatgen
158Skill Claude CodeCodex needs its repo
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
not rated 60 5mo ago A 38 tokens
copy · 91% MIT
Skill Claude CodeCodex
Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
not rated 60 5mo ago A 48 tokens
copy · 84% MIT
pymoo
160Skill Claude CodeCodex needs its repo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
not rated 60 5mo ago A 46 tokens
copy · 95% MIT
pyopenms
161Skill Claude CodeCodex
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and…
not rated 60 5mo ago A 62 tokens
original MIT
pysam
162Skill Claude CodeCodex
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
not rated 60 5mo ago A 47 tokens
copy · 97% MIT
pytdc
163Skill Claude CodeCodex
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
not rated 60 5mo ago A 41 tokens
copy · 88% MIT
Skill Claude CodeCodex
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
not rated 60 5mo ago A 65 tokens
copy · 78% MIT
qiskit
165Skill Claude CodeCodex
IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use…
not rated 60 5mo ago A 73 tokens
copy · 91% MIT
qutip
166Skill Claude CodeCodex
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for…
not rated 60 5mo ago A 72 tokens
copy · 86% MIT
rdkit
167Skill Claude CodeCodex
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom…
not rated 60 5mo ago A 80 tokens
copy · 100% MIT
Skill Claude CodeCodex needs its repo
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
not rated 60 5mo ago B 35 tokens
copy · 100% MIT
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