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DNAnexus Cloud Integration

dnanexus-integration

K-Dense-AI/claude-scientific-skills

Integrate with the DNAnexus cloud genomics platform to build, configure, and run bioinformatics apps, manage FASTQ/BAM/VCF datasets, orchestrate workflows, and script everything through the dxpy Python SDK for automated pipelines.

EDGAR Data Extractor

K-Dense-AI/claude-scientific-skills

Python library for accessing SEC EDGAR filings, extracting XBRL statements, insider trading, and institutional holdings data to power financial analysis, screening, or structured data workflows across 10-K/10-Q/8-K/DEF-14A filings.

FluidSim CFD Framework

K-Dense-AI/claude-scientific-skills

FluidSim is a Python CFD toolkit for pseudospectral Navier-Stokes, shallow-water, and stratified-flow simulations, delivering FFT-based solvers, Pythran/Transonic speedups, MPI scaling, and integrated analysis plus visualization workflows.

Unified Genomics CLI

K-Dense-AI/claude-scientific-skills

gget is a fast CLI and Python package providing unified access to 20+ genomic databases for gene info, BLAST, AlphaFold structures and enrichment lookups, making it ideal for interactive exploration and quick biological queries.

Histolab Tile Toolkit

K-Dense-AI/claude-scientific-skills

Histolab automates tissue detection, tile extraction, and stain normalization on whole slide images so researchers can prep datasets and run lightweight pipelines before diving into advanced spatial or multiplexed analysis.

Document Markdown Converter

K-Dense-AI/claude-scientific-skills

MarkItDown converts PDFs, Office docs, images, audio, HTML, CSV/JSON/XML, archives, and YouTube content into clean Markdown so LLMs can consume structured, token-efficient source material via CLI or Python APIs including OCR, transcription, and AI image captions.

Medchem Filtering Toolkit

K-Dense-AI/claude-scientific-skills

Medchem is a Python library for applying drug-likeness rules, structural alerts, and complexity metrics to triage compound libraries. Run rule sets, catalogs, and custom constraints with parallel filtering, aiding lead optimization and quality control workflows.

Network Analysis Toolkit

K-Dense-AI/claude-scientific-skills

Provides Python-based tools for building, analyzing, and visualizing graph or network data, covering creation, algorithms (shortest paths, centrality, communities), generation, I/O, and rendering for domains like social, biological, or transport systems.

OMERO Microscopy Integration

omero-integration

K-Dense-AI/claude-scientific-skills

OMERO Integration provides a Python-centric bridge to connect with OMERO servers, query microscopy datasets, manipulate pixel and ROI data, attach annotations, and run scripted batch analyses for high-content workflows.

Pydicom Medical Imaging

K-Dense-AI/claude-scientific-skills

Pydicom lets Python programs read, write, and manipulate DICOM medical imaging files, covering pixel extraction, metadata edits, anonymization, format conversion, compression handling, and PACS integration for radiology workflows.

Hardware Agnostic Lab Automation

K-Dense-AI/claude-scientific-skills

PyLabRobot is a Python SDK that controls liquid handlers, plate readers, pumps and other lab automation devices through one unified API, ideal for multi-vendor workflows, simulations, and reproducible protocols across platforms.

Materials Structure Toolkit

K-Dense-AI/claude-scientific-skills

Pymatgen is a Python toolkit for computational materials science that creates, manipulates, and analyzes crystal structures, converts among 100+ formats, computes phase diagrams, and accesses Materials Project data for high-throughput workflows.

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