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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.

Self-Hosted Research Notebook

K-Dense-AI/claude-scientific-skills

Open Notebook is a self-hosted, open-source alternative to NotebookLM that ingests PDFs, videos, audio, and webpages into notebooks, offers a REST API, multi-provider AI, context-aware chat, vector search, and podcast generation for privacy-first research workflows.

Open Targets Explorer API

opentargets-database

K-Dense-AI/claude-scientific-skills

Provides GraphQL queries to the Open Targets Platform for target-disease associations, tractability, safety, drugs, and multi-omics evidence to guide therapeutic target identification, safety assessment, and repurposing research workflows.

Opentrons Protocol Integration

opentrons-integration

K-Dense-AI/claude-scientific-skills

Provides the official Opentrons Protocol API v2 guidance for writing, loading hardware, and executing automated liquid-handling protocols on OT-2 and Flex robots, including module control, labware setup, and advanced pipetting flows.

Protocols.io Integration

protocolsio-integration

K-Dense-AI/claude-scientific-skills

Provides protocols.io API integration for searching, creating, updating, and publishing lab protocols, managing steps, workspaces, discussions, files, and experiment records so teams can automate collaborative protocol workflows.

Pymoo Multi Objective Optimizer

K-Dense-AI/claude-scientific-skills

Pymoo is a Python optimization toolkit focused on multi-objective engineering problems, providing algorithms like NSGA-II/III, MOEA/D, customizable operators, benchmarks, and visualization helpers for Pareto analysis and constrained search.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam provides Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, letting developers query regions, compute coverage, and orchestrate NGS pipelines.

Scanpy Single-Cell Pipeline

K-Dense-AI/claude-scientific-skills

Scanpy provides a scalable Python pipeline for single-cell RNA-seq, covering QC, normalization, dimensionality reduction, clustering, marker discovery, annotation, trajectory analysis, and publication-ready visualizations through AnnData.

Single-Cell Generative Toolkit

K-Dense-AI/claude-scientific-skills

Provides Pythonic probabilistic deep models for single-cell genomics, covering RNA, ATAC, multimodal, and spatial data—all with batch correction, uncertainty-aware differential expression, and scanpy-friendly APIs.

Skill Improvement Loop

trailofbits/skills

Automates iterative use of the plugin-dev skill-reviewer agent to diagnose and fix Claude Code SKILL.md issues, driving repeated review/fix cycles until standards are met before emitting the completion marker.

PyTorch Geometric GNNs

torch-geometric

K-Dense-AI/claude-scientific-skills

PyTorch Geometric provides tooling to build and train graph neural networks over irregular, multi-type graph data, covering dataset loading, message passing layers, mini-batching, and multi-GPU support for social, citation, molecular, and geometric learning workloads.

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