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Annotated Matrix Data Tool

K-Dense-AI/claude-scientific-skills

AnnData offers a Python-native structure for storing annotated matrices with observations, variables, multi-dimensional metadata, and optimized IO, making it ideal for single-cell and large-scale bioinformatics workflows.

Structured Paper Search

bgpt-paper-search

K-Dense-AI/claude-scientific-skills

BGPT Paper Search queries the BGPT MCP server for scientific publications, returning structured metadata such as methods, quantitative results, sample sizes, and quality scores for each full-text study to support reviews, meta-analyses, and evidence synthesis.

bioRxiv Preprint Search

biorxiv-database

K-Dense-AI/claude-scientific-skills

Enables efficient querying of the bioRxiv preprint server with keywords, authors, dates, and categories, returning structured JSON metadata and optional PDF downloads for literature reviews or tracking research trends.

Cellxgene Census API

cellxgene-census

K-Dense-AI/claude-scientific-skills

Programmatically query the 61M+ CELLxGENE Census atlas to access curated single-cell expression matrices, metadata, and embeddings for tissue, disease, and cell type exploration or ML-ready datasets.

Citation Management Assistant

citation-management

K-Dense-AI/claude-scientific-skills

Automates academic citation management by searching Google Scholar and PubMed, extracting metadata from DOIs/PMIDs/arXiv, validating references, and generating properly formatted BibTeX entries to keep research writing accurate.

Scientific Data Exploration

exploratory-data-analysis

K-Dense-AI/claude-scientific-skills

Automates exploratory analysis for 200+ scientific file formats—detecting type, extracting metadata, assessing quality, and producing markdown reports with format-specific insights and recommendations.

FlowIO FCS Handler

K-Dense-AI/claude-scientific-skills

Lightweight Python library to read, inspect, and write FCS v2.0-3.1 files, outputting metadata, channel info, and NumPy arrays for preprocessing cytometry pipelines and backend services.

Genomic Interval ML

K-Dense-AI/claude-scientific-skills

Geniml is a Python toolkit for applying machine learning to genomic interval data (BED/scATAC-seq), offering region and metadata embeddings, universe-building, and utilities for downstream similarity search, clustering, and evaluation.

GWAS Catalog Access

K-Dense-AI/claude-scientific-skills

Query the NHGRI-EBI GWAS Catalog for SNP-trait associations, fetch study metadata, variant and trait details, and download summary statistics via the web or REST APIs to support genetic epidemiology and polygenic risk modeling.

OFR Hedge Fund Monitor

hedgefundmonitor

K-Dense-AI/claude-scientific-skills

Access aggregated OFR hedge fund time series and metadata without auth, covering Form PF stats, repo volumes, futures trader positioning, and leverage/counterparty metrics for risk monitoring or research.

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.

Mass Spectra Matching

K-Dense-AI/claude-scientific-skills

Matchms is an open-source Python toolkit for metabolomics mass spectrometry workflows: import and export diverse spectra, standardize metadata, filter peaks, score spectral similarity (cosine/modified cosine), and build pipelines to identify unknown compounds from libraries.

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