Topic: codex
8,457 skills in this topic.
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hypothesis-generation
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
x-cmd/skill 19
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nu
Enhanced interface for Nushell, enabling x-cmd integration, documentation search, and AI-powered command generation. Core Scenario: When the user needs to set up x-cmd in Nushell or search Nushell documentation via CLI.
x-cmd/skill 19
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speckit
Enhancement module for Spec Kit, helping users set up and use the Specify CLI for spec-driven development. Core Scenario: When the user wants to initialize a Specify project to formalize the "Requirement → Plan → Task → Implementation" flow.
x-cmd/skill 19
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cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
x-cmd/skill 19
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algorithmic-art
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
x-cmd/skill 19
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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
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perplexity-search
Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.
x-cmd/skill 19
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pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
x-cmd/skill 19
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pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
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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adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
x-cmd/skill 19
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pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
x-cmd/skill 19
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datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
x-cmd/skill 19
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brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
x-cmd/skill 19
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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.
x-cmd/skill 19
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stable-baselines3
Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.
x-cmd/skill 19
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research-grants
Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
x-cmd/skill 19
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transformers
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
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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x-cmd
**IMPORTANT**: Before using any `x <mod>` command, you MUST load x-cmd first: `. ~/.x-cmd.root/X`
Then you can:
- Explore with `x nihao --llmstxt`
- Discover skills via `x skill`
x-cmd provides 600+ portable software and development tools (jq, nodejs, python, etc.).
Use `x <env|pixi> use <pkg>` to install and use any package instantly.
After loading x-cmd, packages in x-cmd/pixi's local bin will be automatically available in PATH.
Browse x-cmd website for more usage and skills: https://www.x-cmd.com/llms.txt
x-cmd/skill 19
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anndata
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
x-cmd/skill 19
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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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hostname
Manage the system's hostname, including viewing current name and setting new names. Core Scenario: When the user needs to identify the device name or change the system hostname.
x-cmd/skill 19
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uptime
Display system uptime and load averages in structured YAML format. Core Scenario: When the user needs to check system busy state (load) or total runtime in a script-friendly format.
x-cmd/skill 19