MEMO Publication Examples

Code and Data to reproduce analyses of MEMO paper

This repository contains code to reproduce MEMO analyses. The preprint is available on Biorxiv.

MEMO package repository

MEMO source code is available on Github. It also available as a python package through pip installation.

Interactive HTML plots

Interactive plots are available here.

Steps to Reproduce

1. clone this repo

git clone https://github.com/mandelbrot-project/memo_publication_examples.git or via SSH

2. set the correct environmenet

The requested package can be installed by creating the conda environment and activating it.

Use the following line for environment creation

conda env create -f environment.yml

And this one to activate it

conda activate memo_examples_env

If you need to update the environment run

conda env update --file environment.yml

3. To use tmap_plotter.py

TMAP package is only available on MacOS and Linux. If you are using Windows, you can use WSL. Install TMAP package using:

conda install -c tmap tmap

4. Download the Plant extract dataset data from the MASSive repository

Large files are available on this MASSive repository:

You need to download:

• the aligned feature table and spectra: see details here
• the 1,920 individual .mgf spectra files: see details here

5. Enjoy!