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GeoPandas Spatial Toolkit

K-Dense-AI/claude-scientific-skills

GeoPandas extends pandas with spatial vector data handling, letting teams read/write shapefiles, GeoJSON, GeoPackage and PostGIS, run reprojections, joins, overlays, buffering, and mapping alongside matplotlib/folium/Cartopy.

Gtars Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Gtars is a high-performance Rust toolkit with Python bindings for genomic interval analysis, covering overlap detection, coverage track generation, ML tokenization, fragment scoring, and reference sequence management for computational genomics workflows.

Automated Hypothesis Discovery

K-Dense-AI/claude-scientific-skills

Automates hypothesis generation and testing on tabular datasets by blending LLM-driven data insights with literature synthesis, enabling researchers to explore patterns, validate competing claims, and surface non-redundant ideas across domains like deception detection or content analysis.

Scientific Hypothesis Generation

hypothesis-generation

K-Dense-AI/claude-scientific-skills

Guides structured, testable scientific hypothesis creation from observations and literature; ideal for experiment design, mechanistic exploration, and predictive planning across domains while integrating mandatory AI-generated schematics.

KEGG REST Toolkit

K-Dense-AI/claude-scientific-skills

Direct Python helpers for KEGG's REST API, covering database metadata, listing, search, retrieval, ID conversion, linkage, and drug interactions to power pathway and gene analysis.

Latch Bio Workflows

latchbio-integration

K-Dense-AI/claude-scientific-skills

LatchBio Integration helps build serverless bioinformatics workflows with Python decorators, LatchFile/LatchDir data management, resource tuning, and Nextflow/Snakemake support for production pipelines.

Matplotlib Visualization Guide

K-Dense-AI/claude-scientific-skills

Matplotlib is Python’s foundational plotting toolkit for creating static, animated, and interactive charts with fine-grained control via both pyplot and object-oriented APIs, making it ideal for scientific publications, notebooks, and GUI workflows.

Pathology Imaging Toolkit

K-Dense-AI/claude-scientific-skills

PathML is a Python toolkit for computational pathology, enabling whole-slide image loading, stain-aware preprocessing, spatial graph construction, and machine learning workflows on multiplexed immunofluorescence data.

Plotly Interactive Charts

K-Dense-AI/claude-scientific-skills

Plotly is a Python graphing library for interactive, publication-quality visuals that bring hover, zoom, animation, and dashboard-ready exports to exploratory analysis and presentations.

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 Workflow

K-Dense-AI/claude-scientific-skills

PyDESeq2 brings DESeq2-style differential expression to Python, letting you load bulk RNA-seq counts, filter low-count genes, model single/multi-factor designs, run Wald tests with FDR correction, optionally shrink log-fold changes, and export results for pandas/AnnData 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.

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