Skill UI

AnnData is a specialized Python package designed for managing and analyzing annotated matrices, particularly crucial in single-cell genomics and bioinformatics. It efficiently stores experimental measurements (X) alongside comprehensive metadata (obs, var, obsm, etc.). This skill allows users to read, write, subset, and concatenate large, complex datasets in formats like .h5ad and .zarr, making it essential for scRNA-seq analysis workflows and integration with the scverse ecosystem.

Arboreto is a powerful Python library designed to infer Gene Regulatory Networks (GRNs) from various gene expression datasets, including bulk and single-cell RNA-seq. It employs scalable algorithms like GRNBoost2 and GENIE3 to identify critical transcription factor-target gene relationships. Featuring support for Dask distributed computing, Arboreto is optimized for large-scale, high-throughput transcriptomic analysis.

Astropy is the fundamental Python package for astronomical research and astrophysics data processing. It provides essential tools for handling physical units, performing coordinate transformations across celestial frames (ICRS, Galactic, etc.), managing FITS files, conducting cosmological calculations, and precise time handling. It is indispensable for any task involving celestial coordinates, unit conversions, or analyzing large astronomical catalogs.

A powerful tool for scientific literature review and evidence synthesis. This skill searches a curated database of full-text scientific papers, going beyond traditional abstracts. It extracts and returns highly structured, quantitative data, including methodologies, quantitative results, sample sizes, quality scores, and 25+ metadata fields per paper, making it ideal for meta-analyses and systematic reviews.

Biopython is a robust, comprehensive toolkit for computational molecular biology written in Python. It enables users to manipulate biological sequences (DNA, RNA, protein), parse standard formats (FASTA, GenBank, PDB, etc.), and programmatically access major bioinformatics databases like NCBI via Entrez. This skill is ideal for developing complex bioinformatics pipelines, including sequence alignment, structural analysis, and phylogenetic tree construction.

A comprehensive Python package providing a unified interface to over 40 major bioinformatics web services and databases. Use it for complex biological workflows, including cross-database querying (e.g., UniProt, KEGG, ChEMBL), identifier mapping, protein sequence retrieval, pathway analysis, and running sequence similarity searches like BLAST. It streamlines data integration from multiple life science resources into consistent Python code.

Provides programmatic access to massive, versioned public single-cell and spatial transcriptomics datasets from CZ CELLxGENE. This skill allows users to efficiently query specific subsets of cell metadata, gene expression matrices, embeddings, and summary statistics across various organisms, tissues, and diseases. It is ideal for large-scale, memory-efficient biological research and model training without full dataset downloads.

Generates professional, publication-ready clinical decision support (CDS) documents for pharmaceutical and clinical research settings. Capabilities include biomarker-stratified patient cohort analyses, evidence-based treatment recommendation reports (with GRADE grading), and advanced statistical analyses (e.g., hazard ratios, survival curves). Outputs are optimized for regulatory submissions and medical guidelines.

COBRApy is a powerful Python library for Constraint-Based Reconstruction and Analysis (COBRA). It enables deep dives into cellular metabolism, allowing users to build, simulate, and analyze complex metabolic models (e.g., genome-scale models). Core functionalities include Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), performing gene/reaction knockouts, and optimizing growth media. It supports standard metabolic model formats like SBML, JSON, and YAML.

This tool opens the dedicated Context Mode Insight dashboard in your default browser. Insight serves as the central analytics layer for AI-assisted engineering teams, providing crucial metrics such as per-engineer productive rates, identifying retry waste, detecting blockers, and offering role-narrowed performance views. It is designed to be the single source of truth for comprehensive team performance monitoring and sign-in details.

Dask is a powerful Python library designed for parallel and distributed computing. It allows users to scale existing pandas and NumPy workflows beyond the limits of available RAM, processing massive datasets up to the terabyte scale. It provides specialized APIs (DataFrames, Arrays, Bags) for handling structured, scientific, and unstructured data efficiently across single machines or multi-node clusters.

Datamol provides a simplified, Pythonic abstraction layer over RDKit, making complex molecular operations accessible for chemical data science. It supports core functionalities including SMILES parsing, structure standardization, calculation of molecular descriptors (e.g., LogP, MW), 3D conformer generation, and efficient parallel batch processing. It is ideal for streamlining molecular data handling in drug discovery and chemical research pipelines.