Skill UI

Scanpy is a scalable Python toolkit for single-cell RNA-seq analyses, covering QC, normalization, dimensionality reduction, clustering, marker discovery, annotation, and publication-ready visualization across h5ad/10X/CSV datasets.

Use UMAP for fast nonlinear manifold reduction to produce embeddings that keep local and global structure, making it ideal for visualization, clustering preprocessing, supervised/parametric workflows, or high-dimensional feature engineering.

Geniml is a comprehensive Python package designed for applying machine learning models to genomic interval data, typically stored in BED files. It provides several unsupervised methods—including Region2Vec and BEDspace—to learn robust embeddings of genomic regions, single cells (scATAC-seq), and associated metadata. Use cases include dimensionality reduction, structural variation analysis, cell-type annotation, and cross-modal querying in genomics research.

A comprehensive, scalable Python toolkit designed for end-to-end single-cell RNA-seq data analysis. It supports crucial steps including quality control (QC), normalization, dimensionality reduction (PCA, UMAP, t-SNE), cell clustering, and differential gene expression analysis. The skill provides ready-to-run scripts for analyzing various formats (e.g., .h5ad, 10X, R-native) and generating publication-quality visualizations and cell type annotations.

A comprehensive resource detailing the use of scikit-learn, the industry-standard Python library for classical machine learning. Use this skill for the entire ML lifecycle, including supervised tasks (classification, regression), unsupervised tasks (clustering, dimensionality reduction), data preprocessing, model evaluation, and building production-ready pipelines.

UMAP (Uniform Manifold Approximation and Projection) is a powerful technique for non-linear dimensionality reduction. This skill enables the creation of scalable, structure-preserving embeddings (2D/3D) for visualization, clustering preprocessing, and advanced machine learning feature engineering. It supports various metrics (e.g., Euclidean, Cosine) and supervised learning workflows.