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Topic: codex

8,457 skills in this topic.

deeptools NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
x-cmd/skill 19
diffdock Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
x-cmd/skill 19
dnanexus-integration DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
x-cmd/skill 19
ensembl-database Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
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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
jq Lightweight and flexible JSON processor. Core Scenario: When the AI needs to filter, transform, format, or extract JSON data in the terminal. x-cmd version provides zero-dependency auto-installation.
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fda-database Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
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molfeat Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
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modal Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.
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medchem Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
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matplotlib Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.
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markitdown Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
x-cmd/skill 19
market-research-reports Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix.
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latex-posters Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.
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latchbio-integration Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
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flowio Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
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kegg-database Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
x-cmd/skill 19
deno Enhanced Deno module for running modern JavaScript and TypeScript with zero setup. Core Scenario: When the user needs to execute TypeScript scripts or manage Deno-based applications.
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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.
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gemini Integrate Google Gemini AI for chat, text analysis, and multimodal tasks like image understanding. Core Scenario: When the user wants to use Gemini models for advanced chat, translation with file context, or analyzing images via CLI.
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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.
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gh Enhanced GitHub CLI for managing repositories, issues, PRs, actions, and GitHub Models. Core Scenario: When the user needs to automate GitHub workflows, manage secrets, or use GitHub's AI models via CLI.
x-cmd/skill 19
gitconfig Manage Git configurations using YAML files for structured and portable setup. Core Scenario: When the user needs to apply complex Git configurations or migrate settings via YAML.
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grok Integrate xAI Grok for intelligent chat and real-time information processing. Core Scenario: When the user wants to use Grok models for advanced reasoning or real-time query answers via CLI.
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