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PubMed Database Access

pubmed-database

K-Dense-AI/claude-scientific-skills

Direct REST/API access to PubMed for constructing complex Boolean or MeSH queries, filtering by publication attributes, and automating literature retrieval or citation management via NCBI’s E-utilities.

PyDESeq2 Differential Analysis

K-Dense-AI/claude-scientific-skills

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

Materials Structure Toolkit

K-Dense-AI/claude-scientific-skills

A Python materials science library for constructing, analyzing, and converting crystal structures, computing phase diagrams and electronic properties, and integrating with the Materials Project API for high-throughput workflows.

PyMC Bayesian Modeling

pymc-bayesian-modeling

K-Dense-AI/claude-scientific-skills

Structured workflow for building hierarchical Bayesian models with PyMC 5+, covering data prep, NUTS sampling, diagnostics, posterior checks, and predictive inference.

Pymoo Multi Objective Optimizer

K-Dense-AI/claude-scientific-skills

Python framework for multi-objective optimization, offering NSGA-II/III, MOEA/D, benchmark suites, customizable operators, and visualization to help engineering teams explore Pareto fronts and make multi-criteria decisions.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

Qiskit Quantum Computing Framework

K-Dense-AI/claude-scientific-skills

Qiskit is the world's leading open-source framework for building, optimizing, and executing quantum circuits. It provides comprehensive capabilities for quantum error mitigation, running algorithms on diverse hardware backends (including IBM Quantum and simulators), and supporting applications in chemistry and machine learning. Essential for researchers entering the quantum computing field.

Agency Research Grant Writing

research-grants

K-Dense-AI/claude-scientific-skills

Craft competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC by aligning narratives with agency review criteria, detailing budgets, personnel plans, and broader impacts, and incorporating required AI-generated schematics via the scientific-schematics skill.

Cloud Molecular Modeling Workflows

K-Dense-AI/claude-scientific-skills

Cloud-native Rowan orchestrates medicinal chemistry and molecular modeling pipelines via a Python API, offering pKa prediction, docking, descriptors, dynamics, and AI-driven structure workflows for scalable batch screening without local HPC.

Scientific Critical Thinking

scientific-critical-thinking

K-Dense-AI/claude-scientific-skills

Assess research claims and experimental rigor by evaluating methodology, statistical validity, evidence quality, and biases using GRADE and Cochrane ROB frameworks, plus supporting schematics for complex concepts.

Smart Scientific Diagrams

scientific-schematics

K-Dense-AI/claude-scientific-skills

Use Nano Banana 2 plus Gemini 3.1 Pro Preview to iteratively craft publication-quality scientific schematics—neural nets, pathways, or system diagrams—matching document-type quality thresholds.

Single-Cell Generative Toolkit

K-Dense-AI/claude-scientific-skills

Probabilistic deep-learning framework built on PyTorch for single-cell omics; handles batch correction, integration, multimodal and spatial data, differential expression, and transfer learning with unified APIs.

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