Topic: codex
8,457 skills in this topic.
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gg
Search the web using Google Gemini AI, combining search results with AI-generated answers. Core Scenario: When the user needs real-time information from the web with AI-summarized responses and source citations.
x-cmd/skill 19
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clinvar-database
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
x-cmd/skill 19
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uspto-database
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
x-cmd/skill 19
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cd
Enhanced cd command with history navigation, fuzzy search, and directory aliases. Core Scenario: When the user needs to quickly jump between historical paths or search for subdirectories using keywords.
x-cmd/skill 19
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bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
x-cmd/skill 19
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umap-learn
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
x-cmd/skill 19
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etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
x-cmd/skill 19
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ll
Search and list information about files, archives, and operating system resources using fzf. Core Scenario: When the user needs an interactive way to explore file metadata or system resource summaries.
x-cmd/skill 19
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yq
Portable command-line YAML, JSON, and XML processor with an interactive REPL for exploring data. Core Scenario: When the user needs to query, extract, or interactively browse YAML configurations or structured data.
x-cmd/skill 19
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onsh
Enhanced interface for xonsh, providing x-cmd integration, documentation search, and AI capabilities. Core Scenario: When the user needs to integrate x-cmd with xonsh or search xonsh documentation via CLI.
x-cmd/skill 19
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x-zuz
Unified compression and decompression tool. Core Scenario: When AI needs to handle various archive formats (zip, tar, gz, 7z, rar, zst, xz, bz2) in the terminal. x-cmd provides concise aliases and zero-dependency installation.
x-cmd/skill 19
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pkgx
Universal tool runner for executing any open-source tool without pre-installation or config. Core Scenario: When the user needs to run a CLI tool instantly without modifying their system or PATH.
x-cmd/skill 19
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find
Search for files and directories in a directory hierarchy with an interactive FZF application. Core Scenario: When the user needs to find files based on name, size, type, or other metadata.
x-cmd/skill 19
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bun
High-performance JavaScript runtime and package manager module. Core Scenario: When the user needs an extremely fast JS/TS runtime or package manager for local development.
x-cmd/skill 19
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clinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
x-cmd/skill 19
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rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
x-cmd/skill 19
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matlab
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
x-cmd/skill 19
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aeon
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
x-cmd/skill 19
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labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
x-cmd/skill 19
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sympy
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
x-cmd/skill 19
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pdb-database
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
x-cmd/skill 19
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vaex
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not fit in memory.
x-cmd/skill 19
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gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
x-cmd/skill 19
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biorxiv-database
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
x-cmd/skill 19