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vdjdb-format

Normalize VDJdb TSV chunks to VDJdb and IMGT standards.

155|28|Updated Jan 6, 2016
Search Tags:#bioinformatics#data standardization#VDJdb#IMGT#TCR analysis
One-click install
npx skills add https://github.com/antigenomics/vdjdb-db --skill vdjdb-format
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: vdjdb-format
Source: https://github.com/antigenomics/vdjdb-db/tree/main/skills/vdjdb-format
Command: npx skills add https://github.com/antigenomics/vdjdb-db --skill vdjdb-format

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires vdjdb, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This skill normalizes and standardizes VDJdb TSV chunks, ensuring compatibility and consistency with the VDJdb and IMGT specifications, reducing the time spent on data validation and formatting.

Core Features & Use Cases

  • Standardization of VDJdb Data: Ensures consistency of species names, IMGT V/D/J gene IDs, and MHC alleles according to VDJdb specifications.
  • Species Normalization: Automatically corrects and standardizes species names to their VDJdb-accepted format.
  • IMGT Gene ID Conversions: Converts IMGT V/D/J gene IDs from various formats to the standardized IMGT notation.
  • MHC Allele Standardization: Formats and validates human and mouse MHC alleles to VDJdb/IMGT standards.
  • Method Vocabulary Normalization: Transforms method terms used in TSV chunks into recognized VDJdb/IMGT vocabulary.
  • Chunk ID Renumbering: Sequentially renumbers chunk IDs after standardization.
  • Format Log Generation: Provides a detailed log of changes, discrepancies, and decisions made during standardization.
  • Output Filename Specification: Determines output filenames based on publication IDs, alternative identifiers, or submission data.

Quick Start

Execute the 'vdjdb-format /format path/to/chunk_file.tsv' command to standardize the TSV chunk.

Frequently Asked Questions about vdjdb-format

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

FAQPage Schema
How do I standardize VDJdb TSV chunks for IMGT compatibility?▼

Standardizing VDJdb TSV chunks involves transforming species names, gene IDs, and method terms to adhere to VDJdb and IMGT standards. This process ensures compatibility and consistency during data submissions and updates.

What is the best way to normalize species names and method terms in TCR analysis data?▼

Normalizing species names and method terms in TCR analysis data requires applying standardization rules that correct and format entries to recognized VDJdb and IMGT vocabulary. This reduces time spent on manual data validation and formatting.

How do I convert IMGT gene IDs to standardized notation for VDJdb submissions?▼

Converting IMGT gene IDs to standardized notation involves transforming V/D/J gene identifiers from various formats into the official IMGT notation. This ensures your TCR analysis data meets VDJdb submission specifications.

Can I format human and mouse MHC alleles to VDJdb standards automatically?▼

Yes, you can automatically format and validate human and mouse MHC alleles to VDJdb and IMGT standards. The formatting process ensures alleles adhere to the required specifications for consistent data submissions.

Does the VDJdb format tool require the vdjdb dependency to standardize TSV files?▼

Yes, standardizing VDJdb TSV chunks requires the vdjdb dependency. The process relies on normalization rules, IMGT gene authority data, and method vocabulary logic to transform and validate the data correctly.

Why are chunk IDs renumbered during VDJdb TSV data standardization?▼

Chunk IDs are sequentially renumbered during VDJdb TSV data standardization to maintain order after the transformation process. A detailed format log is also generated to track changes, discrepancies, and decisions made.

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