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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.

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.

PyOpenMS Mass Spectrometry

K-Dense-AI/claude-scientific-skills

PyOpenMS exposes OpenMS via Python to cover end-to-end proteomics and metabolomics workflows, including file I/O, signal processing, feature detection, identification, quantitation, and integration with pandas/visualization stacks.

Therapeutics Data Commons

K-Dense-AI/claude-scientific-skills

PyTDC offers curated AI-ready datasets, standardized benchmarks, and scaffold-aware splits across ADME, toxicity, interaction, and generation tasks to support therapeutic ML and pharmacological prediction workflows.

Scikit Learn ML Guide

K-Dense-AI/claude-scientific-skills

Comprehensive guidance for building classical machine learning workflows with scikit-learn, spanning supervised and unsupervised algorithms, preprocessing, evaluation, tuning, and production-ready pipelines for structured or text data.

TileDB VCF Storage

K-Dense-AI/claude-scientific-skills

TileDB-VCF lets you ingest, store, query, and export large genomic VCF/BCF datasets using TileDB’s sparse arrays, supporting incremental sample growth, parallel regions queries, and cloud-local interoperability for population genomics workflows.

UniProt Rest Access

uniprot-database

K-Dense-AI/claude-scientific-skills

Direct REST API access to UniProt for searching proteins, fetching FASTA sequences, mapping identifiers, selecting annotations, and streaming large datasets within Python workflows.

Vaex Big Data

K-Dense-AI/claude-scientific-skills

Vaex processes massive tabular datasets (billions of rows) with lazy, out-of-core DataFrames, fast aggregations, visualization, and ML pipelines without fitting data into memory, ideal for CSV/Arrow/Parquet workflows.

Zarr Python Arrays

K-Dense-AI/claude-scientific-skills

Handles chunked, compressed N-D arrays in Python for cloud-friendly workflows; integrates seamlessly with NumPy, Dask, and Xarray to enable parallel I/O, sharding, and persistence to S3/GCS for large-scale scientific pipelines.

GeoMaster Spatial Intelligence Suite

K-Dense-AI/claude-scientific-skills

GeoMaster delivers a comprehensive geospatial science skill set for remote sensing, GIS, spatial analysis, and ML workflows using satellite imagery, point clouds, and cloud-native catalogs across 8 languages with 500+ code examples for Earth observation applications.

InterPro Protein Annotation

interpro-database

K-Dense-AI/claude-scientific-skills

Query InterPro for protein family, domain, and GO annotations via a REST API with Python helpers, enabling function prediction, domain architecture mapping, and evolutionary classification insights for proteomic workflows.

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