Lyso-IP Organelle Coverage

Installation

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

Repository: https://github.com/noatgnu/lysoip-organelle-coverage-plugin

Manual installation:

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

ID: lysoip-organelle-coverage
Version: 1.0.0
Category: lysoip-qc
Author: CauldronGO Team

Description

Two one-sided Fisher's exact tests asking whether marker genes clear the Positive/Negative gate more often than the run's own background, optionally ranked across every curated list

Workflow Diagram

flowchart TD
    Start([Start]) --> step1
    step1["Loading verdicts"]
    step1 --> load_lists
    load_lists["Loading organelle marker lists"]
    load_lists --> test_all
    test_all{"Test all curated lists?"}
    test_all -->|"yes"| test_all_lists
    test_all -->|"no"| test_one_list
    test_all_lists["Testing coverage against every curated list"]
    test_all_lists --> step2
    test_one_list["Testing coverage against the target list"]
    test_one_list --> step2
    step2["Applying BH-FDR correction and ranking"]
    step2 --> End([End])

Runtime

• Environments: python

• Entrypoint: lysoip_organelle_coverage.py

Inputs

Input Details

Verdicts (verdict_file)

verdict.tsv from the Lyso-IP Gating & Ranking plugin

Expected Organelle List (organelle_list)

Curated marker-gene list bundled with this plugin, same source as the Lyso-IP Organelle Specificity plugin

• Options: LSD (Platt 2018) (LSD (Platt 2018) (53 genes)), Lysosome (Hein 2025) (Lysosome (Hein 2025) (158 genes)), LSD + Lysosome (LSD + Lysosome (180 genes)), ER (Hein 2025) (ER (Hein 2025) (349 genes)), Golgi (Hein 2025) (Golgi (Hein 2025) (87 genes)), Endosome (Park and Itzhak 2022) (Endosome (Park and Itzhak 2022) (93 genes)), Mitochondria (Rath 2021) (Mitochondria (Rath 2021) (1136 genes)), Ribosome (Nakao 2004) (Ribosome (Nakao 2004) (80 genes)), Nucleus (Leung 2006) (Nucleus (Leung 2006) (410 genes))

Test Against Every List (test_all_lists)

When enabled, tests coverage against every curated list (not just the expected one), BH-FDR corrects across the panel, and ranks best-match-first — useful for diagnosing a mismatched or contaminated sample

Coverage Alpha (coverage_alpha)

p-value threshold for calling a list's enrichment significant

Outputs

Requirements

• Python Version: >=3.11

Package Dependencies (Inline)

Packages are defined inline in the plugin configuration:

• scipy>=1.11.0

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:

  verdict_file: examples/verdict.tsv
  organelle_list: LSD + Lysosome
  test_all_lists: true

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

Usage

Via UI

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

Via Plugin System

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