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Annotated Data Matrix

K-Dense-AI/claude-scientific-skills

AnnData supplies a Python-native container for annotated matrices, letting researchers store measurements alongside rich metadata, read/write h5ad/zarr/loom/10X files, and integrate with the scverse tools when building single-cell or related data workflows.

Benchling Integration Toolkit

benchling-integration

K-Dense-AI/claude-scientific-skills

Automate Benchling lab data workflows via the Python SDK or REST API: manage registry entities (DNA, proteins), inventory, ELN entries, workflows, and Data Warehouse queries for syncing and analytics.

Biopython Molecular Toolkit

K-Dense-AI/claude-scientific-skills

Biopython provides Python APIs for sequence manipulation, database access, BLAST automation, structural bioinformatics, and phylogenetics, making it ideal for scripting custom pipelines and batch processing in computational molecular biology workflows.

Scaling Pandas with Dask

K-Dense-AI/claude-scientific-skills

Dask is a Python library that scales pandas/NumPy workflows beyond RAM by parallelizing DataFrames, Arrays, Bags, and custom tasks across cores or clusters for ETL, log analysis, and distributed ML.

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.

OMERO Microscopy Integration

omero-integration

K-Dense-AI/claude-scientific-skills

Manage microscopy data with the OMERO Python API: access projects/datasets/images, retrieve and analyze pixel data, handle ROIs and annotations, store results in tables, and automate batch workflows for high-content screening.

PubChem Database Query

pubchem-database

K-Dense-AI/claude-scientific-skills

Leverages PubChem’s PUG-REST API or PubChemPy to search 110M+ compounds by name, CID, or structure, fetch properties, perform similarity/substructure lookups, and access bioactivity or format conversions for cheminformatics workflows.

PyOpenMS Mass Spectrometry

K-Dense-AI/claude-scientific-skills

PyOpenMS provides Python bindings for OpenMS to drive complete mass spectrometry workflows, covering data IO, spectral processing, feature/peptide-protein identification, quantitation, and metabolomics pipelines.

PyTorch Lightning Toolkit

pytorch-lightning

K-Dense-AI/claude-scientific-skills

PyTorch Lightning Toolkit streamlines PyTorch model training by organizing LightningModules, LightningDataModules, Trainer configs, callbacks, logging, and distributed strategies for scalable multi-GPU/TPU runs in research or production workflows.

Zeroization Audit Tool

trailofbits/skills

Detects missing zeroization of secrets and flags compiler-optimized removals with mandatory assembly/IR evidence, helping auditors verify C/C++/Rust cryptographic code through dataflow, CFG, and runtime validation.

Zotero Reference Management Python Wrapper

K-Dense-AI/claude-scientific-skills

A robust Python client wrapper for interacting with the Zotero Web API v3. This skill allows users to programmatically manage academic references, including retrieving, creating, updating, and deleting items, collections, tags, and attachments. Ideal for academic researchers building automated workflows, bulk exporting citations (e.g., BibTeX), or integrating Zotero data into larger research applications.

Apify Actor Development and Deployment

apify-actor-development

sickn33/antigravity-awesome-skills

This guide provides a comprehensive walkthrough for developing and deploying Apify Actors. Actors are serverless, containerized applications designed for powerful tasks like web scraping, data processing, and complex automation. Learn the mandatory setup, template selection (Python, JS, TS), step-by-step development workflow, and crucial security best practices for building robust, production-ready data pipelines.

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