Skill UI

Aeon is a comprehensive, scikit-learn compatible Python toolkit designed for advanced time series machine learning. It supports a wide range of temporal tasks, including classification, regression, clustering, forecasting, anomaly detection, and pattern recognition. Ideal for analyzing sequential data and extracting features from time-indexed observations.

AnnData is a core Python framework designed for managing and analyzing annotated matrices, essential in single-cell genomics and high-dimensional data science. It provides a standardized structure (X, obs, var) to store experimental measurements alongside rich metadata. Users can read/write various formats (h5ad, zarr), perform subsetting, concatenation, and complex data manipulation, making it indispensable for modern bioinformatics workflows.

Arboreto is a powerful Python library designed for inferring Gene Regulatory Networks (GRNs) from various gene expression datasets, including bulk and single-cell RNA-seq data. It leverages advanced machine learning algorithms like GRNBoost2 and GENIE3. The library supports scalable, distributed computation using Dask, making it ideal for analyzing large-scale, complex transcriptomics datasets to identify critical transcription factor-target gene relationships.

A powerful tool designed for systematic literature reviews and meta-analyses. It searches scientific papers and retrieves highly structured experimental data directly from the full text, going beyond mere abstracts. It extracts over 25 fields, including detailed methods, quantitative results, sample sizes, quality scores, and conclusions, enabling comprehensive evidence synthesis for academic research.

Provides programmatic and standardized access to massive, versioned datasets of single-cell and spatial transcriptomics from CZ CELLxGENE. This skill allows users to query millions of cells, analyze gene expression, and access pre-calculated embeddings across various tissues, diseases, and species without downloading entire datasets. Essential for large-scale bioinformatics analysis, machine learning model training, and comprehensive cross-dataset comparison.

This skill generates safety-bounded draft structures and deterministic checks for various clinical, safety, and aggregate research reports (e.g., CSR, aggregate safety tables). It requires verified, de-identified, or synthetic source data, ensuring every generated claim is traceable to a source-fact manifest. IMPORTANT: This skill only creates drafts and checks internal consistency; it cannot diagnose, recommend treatment, or provide medical advice. All outputs are non-clinical and require qualified human review and sign-off.

An autonomous research agent that plans complex investigations using Directed Acyclic Graphs (DAGs). It executes sub-questions in parallel, performs gap analysis, and iteratively refines findings before synthesizing a comprehensive, structured report. Ideal for deep market analysis, academic literature reviews, or complex problem-solving requiring multiple data sources.

DeepChem is a comprehensive Python library designed to apply machine learning to chemistry, materials science, and biology. It enables sophisticated molecular property prediction (ADMET, solubility, toxicity), drug discovery, and materials design. The library supports diverse featurization methods (fingerprints, graph representations) and advanced model architectures, including GNNs and transfer learning, making it ideal for analyzing complex chemical datasets like MoleculeNet.

A comprehensive skill for building, operating, and automating complex, reproducible genomics workloads on the DNAnexus platform. It provides deep integration with the `dx` CLI, `dxpy` Python SDK, and workflow languages like Nextflow and WDL. Use it for data transfer, job monitoring, project automation, and ensuring secure, efficient execution of large-scale biological computations.

This skill provides bounded, local exploratory data analysis for diverse scientific data files, including CSV, JSON, HDF5, and image metadata. It rigorously audits data structure, detects missing values, and identifies outliers in a secure, sandboxed environment. It is designed exclusively for pre-modeling data integrity checks and must not be used to infer scientific meaning or make causal claims.

FlowIO is a specialized, low-level library designed for reading, inspecting, and writing Flow Cytometry Standard (FCS) files (versions 2.0, 3.0, and 3.1). It allows users to extract event data as NumPy arrays, inspect detailed metadata (HEADER, TEXT, ANALYSIS), and handle multi-dataset structures. It is crucial for data preparation, format conversion, and foundational metadata management in bioinformatics pipelines, but does not perform complex analysis like gating or compensation.

Geniml provides a robust framework for running machine learning and statistical workflows over genomic interval sets. It treats coordinates, assemblies, and model artifacts as explicit contracts, enabling users to validate data structures (like BED files) and plan complex runs (such as Region2Vec or scEmbed) locally. The tool emphasizes reproducibility, adherence to biological data standards, and running without unnecessary network calls.