Lyso-IP Differential Expression

Installation

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

Repository: https://github.com/noatgnu/lysoip-differential-expression-plugin

Manual installation:

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

ID: lysoip-differential-expression
Version: 1.0.0
Category: lysoip-qc
Author: CauldronGO Team

Description

Log2 fold-change and significance (limma or msqrob2, auto-selected) plus a ROAST-based whole-run experiment validity test for lyso-IP data

Workflow Diagram

flowchart TD
    Start([Start]) --> load
    load["Loading samples and abundance data"]
    load --> check
    limma_gate["Gating proteins by per-group replicate count"]
    limma_gate --> limma
    limma["Running limma differential expression"]
    limma --> limma_roast
    limma_roast["Running ROAST experiment validity test"]
    limma_roast --> step1
    msqrob2_load["Loading peptide-level abundance"]
    msqrob2_load --> gate
    gate{"Gating peptides by per-group completeness"}
    gate --> single_feature_gate
    gate --> msqrob2
    single_feature_gate["Dropping proteins below the minimum unique peptide count"]
    single_feature_gate --> End([End])
    msqrob2["Running msqrob2 differential expression"]
    msqrob2 --> msqrob2_roast
    msqrob2_roast["Running ROAST experiment validity test"]
    msqrob2_roast --> step1
    check{"Has peptide-level data?"}
    check -->|"no"| limma_gate
    check -->|"yes"| msqrob2_load
    step1["Differential expression complete"]
    step1 --> End([End])

Runtime

• Environments: r

• Entrypoint: lysoip_differential_expression.R

Inputs

Input Details

Protein Abundance (Long Format) (abundance_long_file)

abundance_long.tsv from the Lyso-IP Ingestion plugin

Samples (samples_file)

samples.tsv from the Lyso-IP Ingestion plugin

Peptide Abundance (Long Format) (peptide_abundance_file)

peptide_abundance_long.tsv from the Lyso-IP Ingestion plugin. When given, uses msqrob2 instead of limma.

msqrob2 Imputation Method (impute_method)

Only used when peptide-level data is given. The left-censored methods (MinDet, MinProb, QRILC) assume a missing value is genuinely below detection, not randomly missing.

• Options: MinDet (MinDet (left-censored, recommended for missing-not-at-random)), MinProb (MinProb (left-censored, stochastic)), QRILC (QRILC (left-censored, quantile regression)), knn (k-nearest neighbours), bpca (Bayesian PCA), MLE (Maximum likelihood (EM algorithm)), nbavg (Neighbour averaging), min (Smallest observed value), zero (Zero), none (None (complete-case aggregation only))

Minimum Peptide Completeness (min_completeness)

A peptide needs at least this fraction of replicates present in both the IP and WCL group to be used; only relevant when peptide-level data is given

Minimum Unique Peptides (min_unique_peptides)

A protein needs at least this many distinct qualifying peptides to be tested; only relevant when peptide-level data is given

ROAST Rotations (n_rotations)

Number of rotations for the ROAST experiment-validity test

Minimum Proteins for Validity Test (min_proteins_for_validity)

Experiment validity is undetermined (not failed) below this many tested proteins

Validity Alpha (validity_alpha)

ROAST p-value threshold below which the run is considered to show real differential signal

Outputs

Requirements

• R Version: >=4.0

R Dependencies (External File)

Dependencies are defined in: r-packages.txt

• limma
• jsonlite
• QFeatures
• msqrob2

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:

  abundance_long_file: examples/abundance_long.tsv
  samples_file: examples/samples.tsv
  peptide_abundance_file: examples/peptide_abundance_long.tsv

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

Usage

Via UI

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

Via Plugin System

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