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affinity-proteomics

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Analyze affinity-based proteomics data with platform-aware QC and visualization.

Data & Analytics#data visualization#bioinformatics#proteomics#differential abundance#affinity proteomics
AuthorMubasherMohammed
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This Skill simplifies the analysis of affinity-based proteomics data, providing platform-aware quality control, normalization, differential abundance testing, and visualization.

Core Features & Use Cases

  • Platform-Aware Analysis: Supports Olink NPX and SomaLogic ADAT platforms with specific QC and normalization methods.
  • Differential Abundance Testing: Perform t-test or Mann-Whitney U tests with FDR correction.
  • Visualization: Generate volcano plots, heatmaps, and PCA plots for data visualization.
  • Use Case: Imagine you have affinity proteomics data from Olink and SomaLogic platforms. Use this Skill to analyze the data, identify differentially abundant proteins, and visualize the results.

Quick Start

Run the affinity-proteomics skill on your data with the following command:

python skills/affinity-proteomics/affinity_proteomics.py --platform olink --input data.csv --meta meta.csv --group-col Group --contrast "Case,Control" --output results/

Dependency Matrix

Required Modules

somadatascipystatsmodelsseabornscikit-learnnumpypandasmatplotlib

Components

scriptsreferences

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: affinity-proteomics
Download link: https://github.com/MubasherMohammed/opencode-BioInfo/archive/main.zip#affinity-proteomics

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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