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vdjdb-harmonize

Normalize antigen.gene and antigen.species fields in VDJdb chunks to canonical naming.

155|28|Updated Jan 6, 2016
Search Tags:#harmonization#data normalization#vdjdb#tcr specificity#database processing
One-click install
npx skills add https://github.com/antigenomics/vdjdb-db --skill vdjdb-harmonize
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: vdjdb-harmonize
Source: https://github.com/antigenomics/vdjdb-db/tree/main/skills/vdjdb-harmonize
Command: npx skills add https://github.com/antigenomics/vdjdb-db --skill vdjdb-harmonize

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the harmonization of antigen.gene and antigen.species fields in VDJdb chunks, ensuring consistency and accuracy in TCR specificity reporting.

Core Features & Use Cases

  • Harmonization: Normalize gene and species names to the VDJdb canonical vocabulary.
  • Spurious Detection: Detects and resolves inconsistencies and spurious values.
  • Use Case: Harmonize a VDJdb chunk by running the /harmonize command with the path to the chunk file.

Quick Start

Harmonize a VDJdb chunk by running /harmonize path/to/chunk.tsv.

Frequently Asked Questions about vdjdb-harmonize

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I normalize antigen gene and species fields in VDJdb data?▼

You can normalize VDJdb antigen gene and species fields by running a harmonization command on your chunk file, which resolves spurious values to canonical VDJdb naming conventions.

What is VDJdb antigen species harmonization and when do I need it?▼

VDJdb antigen species harmonization standardizes gene and species names to a canonical vocabulary, needed when processing TCR specificity data chunks that contain inconsistent or spurious naming values.

How do I detect spurious values in a VDJdb chunk file?▼

You detect spurious values in a VDJdb chunk file by applying an automated harmonization process that identifies inconsistencies and resolves them against canonical VDJdb lookup tables.

Do I need lookup tables to harmonize VDJdb antigen data?▼

Yes, harmonizing VDJdb antigen data requires access to lookup tables and patch files, as these resources provide the canonical naming references needed to resolve inconsistencies and spurious values.

What's the best way to resolve inconsistencies in TCR specificity data?▼

The best way to resolve inconsistencies in TCR specificity data is to automate the harmonization of antigen fields, normalizing them against canonical VDJdb naming conventions using lookup tables.

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