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hvantk:resource-cptac-phospho

Retrieve CPTAC phosphoproteomics data and transform it into AnnData and TSV formats.

Updated Feb 2, 2024
Search Tags:#bioinformatics#proteomics#anndata#multiomics#cptac#phosphoproteomics
One-click install
npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-cptac-phospho
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hvantk:resource-cptac-phospho
Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/cptac/phospho
Command: npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-cptac-phospho

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires cptac, pandas, anndata, and includes scripts (resource) components.

What problem does it solve?

This skill automates the complex process of fetching, parsing, and building standardized phosphoproteomics datasets from the CPTAC consortium, bridging the gap between raw mass spectrometry data and downstream multiomics analysis.

Core Features & Use Cases

  • Automated Data Acquisition: Fetches per-cancer phosphoproteomics data directly from the CPTAC Python package.
  • Standardized Matrix Construction: Transforms raw MultiIndex data into clean, analysis-ready AnnData objects and intermediate TSVs.
  • Use Case: Researchers can use this skill to quickly generate a site-level intensity matrix for a specific cancer type, such as BRCA, to correlate phosphorylation sites with genomic variant data in the hvantk PTM pipeline.

Quick Start

Use the hvantk reprocess command to download and build the CPTAC phosphoproteomics dataset for the breast cancer type.

Frequently Asked Questions about hvantk:resource-cptac-phospho

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

FAQPage Schema
How do I convert CPTAC phosphoproteomics data into an AnnData format for multiomics analysis?▼

To convert CPTAC phosphoproteomics data into AnnData format, you can use this skill to automate retrieval and transform raw MultiIndex mass spectrometry data into standardized, analysis-ready matrices for downstream integration.

What is the best way to extract site-level intensity matrices for specific cancer types from CPTAC?▼

The best way to extract site-level intensity matrices for specific cancer types from CPTAC is by using automated per-cancer-type data extraction tools that parse raw phosphoproteomics data into clean TSV files and AnnData objects.

Does the hvantk:resource-cptac-phospho skill require the cptac Python package to fetch proteomics data?▼

Yes, this skill requires the cptac Python package to fetch per-cancer phosphoproteomics data directly from the CPTAC consortium, providing robust error handling for upstream data inconsistencies during retrieval.

Can I integrate CPTAC phosphoproteomics with genomic variant data in a PTM pipeline?▼

Yes, you can integrate CPTAC phosphoproteomics with genomic variant data by generating standardized site-level intensity matrices that serve as direct inputs for downstream PTM pipeline correlation analyses.

Why does CPTAC phosphoproteomics data retrieval fail with upstream data inconsistencies?▼

CPTAC phosphoproteomics data retrieval can fail due to upstream data inconsistencies in the raw mass spectrometry outputs, which this skill addresses by providing robust error handling during the MultiIndex parsing process.

How do I download and build a breast cancer phosphoproteomics dataset from CPTAC?▼

You can download and build a breast cancer phosphoproteomics dataset from CPTAC by running the hvantk reprocess command, which automates fetching and transforming BRCA data into analysis-ready matrices.

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