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Histolab WSI Tile Processing

K-Dense-AI/claude-scientific-skills

Histolab streamlines whole-slide microscopy by automating tissue detection, tile extraction, and stain normalization for H&E scans, making it ideal for lightweight dataset prep and quick tile-based analysis.

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.

NeuroKit2 Biosignal Processing

K-Dense-AI/claude-scientific-skills

NeuroKit2 is a Python biosignal processing toolkit for ECG, EEG, EDA, RSP, EMG, and EOG data that automates cleaning, feature extraction, and HRV/complexity analysis for psychophysiology, clinical, and HCI studies.

Neuropixels Analysis Toolkit

neuropixels-analysis

K-Dense-AI/claude-scientific-skills

End-to-end Neuropixels recording analysis covering SpikeGLX/OpenEphys/NWB loading, preprocessing, motion correction, Kilosort4 sorting, quality metrics, Allen/IBL curation, and AI-assisted visualization for extracellular electrophysiology.

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.

PyDESeq2 Differential Analysis

K-Dense-AI/claude-scientific-skills

PyDESeq2 brings the DESeq2 differential expression workflow to Python, letting users load bulk RNA-seq counts, specify design formulas, fit DESeq2 models, run Wald tests with FDR correction, optionally apply apeGLM shrinkage, and export gene-level statistics within pandas/AnnData pipelines.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

QuTiP Quantum Toolbox

K-Dense-AI/claude-scientific-skills

QuTiP is a Python toolbox for simulating open and closed quantum systems, offering solvers for master equations, trajectory methods, visualization, and analysis tailored to quantum research, education, and exploratory physics studies.

Reactome Pathway Explorer

reactome-database

K-Dense-AI/claude-scientific-skills

Query the Reactome Content and Analysis Services (or the reactome2py client) to fetch pathway hierarchies, map genes, run overrepresentation/expression analyses, and explore disease interactions for systems biology research.

Scikit Survival Analysis

scikit-survival

K-Dense-AI/claude-scientific-skills

Toolkit for Python-based survival and time-to-event modeling with scikit-survival, supporting Cox models, ensemble learners, SVMs, and evaluation metrics for censored data.

Seaborn Statistical Visualization Library

K-Dense-AI/claude-scientific-skills

Seaborn is a powerful Python library for creating publication-quality statistical graphics. It is designed for dataset-oriented plotting, making it ideal for exploratory data analysis, multivariate analysis, and visualizing complex relationships, distributions, and comparisons with minimal code. It builds upon Matplotlib, offering high-level interfaces for functions like scatterplots, heatmaps, and pair plots.

Statistical Analysis and Reporting Guide

statistical-analysis

K-Dense-AI/claude-scientific-skills

A comprehensive guide for systematic statistical analysis, designed for academic research. This skill assists in selecting the correct hypothesis tests (t-test, ANOVA, regression, chi-square), checking assumptions (normality, homogeneity), performing advanced analyses (Bayesian methods, power analysis), calculating effect sizes, and generating full APA-formatted reports for publication.

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