Lyso-IP GO Evidence

Version: 1.0.0

Commit Hash: a9e84c9a88e3ee5e61de739df36a4e067d2f752e

Author: CauldronGO Team

Category: lysoip-qc

goatools enrichment test for the expected subcellular-compartment GO term(s), default lysosomal. Downloads ~47MB of GO reference data on first run and caches it locally (~200MB uncompressed).

Install with Cauldron get_app
README

Lyso-IP GO Evidence

Installation

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

Repository: https://github.com/noatgnu/lysoip-go-evidence-plugin

Manual installation:

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

ID: lysoip-go-evidence
Version: 1.0.0
Category: lysoip-qc
Author: CauldronGO Team

Description

goatools enrichment test for the expected subcellular-compartment GO term(s), default lysosomal. Downloads ~47MB of GO reference data on first run and caches it locally (~200MB uncompressed).

Workflow Diagram

flowchart TD
    Start([Start]) --> step1
    step1["Fetching GO reference data"]
    step1 --> step2
    step2["Loading GO ontology and annotations"]
    step2 --> load_genes
    load_genes["Loading protein/gene list"]
    load_genes --> has_annotations
    has_annotations{"Any study proteins have GO annotations?"}
    has_annotations -->|"no"| step3
    has_annotations -->|"yes"| step4
    step3["Writing empty result"]
    step3 --> End([End])
    step4["Running GO enrichment study"]
    step4 --> step5
    step5["Writing GO evidence scores"]
    step5 --> End([End])

Runtime

  • Environments: python

  • Entrypoint: lysoip_go_evidence.py

Inputs

Name Label Type Required Default Visibility
gene_lookup_file Protein / Gene List file Yes - Always visible
expected_go_terms Expected GO Terms text No GO:0005764,GO:0005765,GO:0043202,GO:0007041 Always visible

Input Details

Protein / Gene List (gene_lookup_file)

Any tidy file with protein and gene columns, e.g. abundance_long.tsv or differential_expression.tsv from earlier lysoip-* plugins

Expected GO Terms (expected_go_terms)

Comma-separated GO term IDs for the expected compartment. Default: lysosome, lysosomal membrane, lysosomal lumen, lysosomal transport.

Outputs

Name File Type Format Description
go_evidence go_evidence.tsv data tsv Per-protein GO evidence score (-log10 of the best BH-FDR q-value among matched expected terms); proteins with no match get no row

Requirements

  • Python Version: >=3.11

Python Dependencies (External File)

Dependencies are defined in: requirements.txt

  • goatools>=1.4.0

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:

  gene_lookup_file: examples/gene_lookup.tsv

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

Usage

Via UI

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

Via Plugin System

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