Lyso-IP Gating & Ranking

Installation

⬇️ Click here to install in Cauldron (requires Cauldron to be running)

Repository: https://github.com/noatgnu/lysoip-gating-ranking-plugin

Manual installation:

1. Open Cauldron
2. Go to Plugins → Install from Repository
3. Paste: https://github.com/noatgnu/lysoip-gating-ranking-plugin
4. Click Install

ID: lysoip-gating-ranking
Version: 1.0.0
Category: lysoip-qc
Author: CauldronGO Team

Description

Classifies proteins as Positive/Negative/Nonsignificant on hard significance gates, then z-score composite-ranks each gated pool

Workflow Diagram

flowchart TD
    Start([Start]) --> step1
    step1["Loading differential expression"]
    step1 --> step2
    step2["Loading optional scorer outputs"]
    step2 --> step3
    step3["Gating proteins on significance and fold-change magnitude"]
    step3 --> step4
    step4["Ranking within each gated pool"]
    step4 --> step5
    step5["Writing verdicts"]
    step5 --> End([End])

Runtime

• Environments: python

• Entrypoint: lysoip_gating_ranking.py

Inputs

Input Details

Differential Expression (differential_expression_file)

differential_expression.tsv from the Lyso-IP Differential Expression plugin (carries fold_change and significance)

Reproducibility Scores (reproducibility_file)

reproducibility.tsv from the Lyso-IP Reproducibility plugin

Organelle Specificity Scores (organelle_specificity_file)

organelle_specificity.tsv from the Lyso-IP Organelle Specificity plugin

GO Evidence Scores (go_evidence_file)

go_evidence.tsv from the Lyso-IP GO Evidence plugin

CompPASS Scores (compass_file)

A TSV with protein, gene, compass columns (CompPASS WD-score)

CRAPome/SAINT Scores (crapome_file)

A TSV with protein, gene, crapome columns (SAINT interaction probability)

Minimum |log2 Fold Change| (fold_change_min_abs_log2)

A protein must clear this magnitude to gate as Positive/Negative

Significance Alpha (significance_alpha)

A protein must clear this adjusted p-value to gate as Positive/Negative

Fold Change Weight (weight_fold_change)

Reproducibility Weight (weight_reproducibility)

Organelle Specificity Weight (weight_organelle_specificity)

GO Evidence Weight (weight_go_evidence)

CompPASS Weight (weight_compass)

CRAPome/SAINT Weight (weight_crapome)

Outputs

Requirements

• Python Version: >=3.11

Package Dependencies (Inline)

Packages are defined inline in the plugin configuration:

• pandas>=2.0.0

Note: When you create a custom environment for this plugin, these dependencies will be automatically installed.

Example Data

This plugin includes example data for testing:

  go_evidence_file: examples/go_evidence.tsv
  compass_file: examples/compass.tsv
  crapome_file: examples/crapome.tsv
  differential_expression_file: examples/differential_expression.tsv
  reproducibility_file: examples/reproducibility.tsv
  organelle_specificity_file: examples/organelle_specificity.tsv

Load example data by clicking the Load Example button in the UI.

Usage

Via UI

1. Navigate to lysoip-qc → Lyso-IP Gating & Ranking
2. Fill in the required inputs
3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('lysoip-gating-ranking', {
  // Add parameters here
});