Protein Coverage Map

Version: 1.0.0

Commit Hash: ae25cbc420c2036a78db3d40261bac7210d2b4ff

Author: Cauldron Team

Category: utilities

Generate protein coverage maps from peptide data with intensity values

Install with Cauldron get_app
README

Protein Coverage Map

Installation

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

Repository: https://github.com/noatgnu/coverage-map-plugin

Manual installation:

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

ID: coverage-map
Version: 1.0.0
Category: utilities
Author: Cauldron Team

Description

Generate protein coverage maps from peptide data with intensity values

Runtime

  • Environments: python

  • Entrypoint: get_coverage.py

Inputs

Name Label Type Required Default Visibility
input_file Input File file Yes - Always visible
sequence_column Peptide Sequence Column column Yes - Always visible
index_column Index Column column Yes - Always visible
uniprot_acc_column UniProt Accession Column column Yes - Always visible
value_columns Intensity/Value Columns multi-column Yes - Always visible
fasta_file FASTA File (Optional) file No - Always visible

Input Details

Input File (input_file)

Tab-separated or CSV file containing peptide data with intensity values

Peptide Sequence Column (sequence_column)

Column containing peptide sequences

Index Column (index_column)

Column to use as peptide identifier/index

UniProt Accession Column (uniprot_acc_column)

Column containing UniProt accession IDs

Intensity/Value Columns (value_columns)

Columns containing intensity or abundance values (comma-separated)

FASTA File (Optional) (fasta_file)

Optional FASTA file with protein sequences. If not provided, sequences will be fetched from UniProt.

Outputs

Name File Type Format Description
coverage.txt coverage.txt data tsv Tab-separated file with coverage map data
uniprot_data.txt uniprot_data.txt data tsv UniProt sequence data used for mapping

Requirements

  • Python Version: >=3.10

Python Dependencies (External File)

Dependencies are defined in: requirements.txt

  • pandas>=2.0.0
  • click>=8.0.0
  • uniprotparser>=1.0.0
  • numpy>=1.24.0

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

Usage

Via UI

  1. Navigate to utilities → Protein Coverage Map
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

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