This repository is the source code for the R package vngMoM which provides helper functions for analysing mother machine data obtaine with the image analysis software (deep)MoMA, as well as a template project for analysing such data (in the example subdirectory). Most of this R code rely heavily on the tidyverse libraries. Getting familiar with those first, e.g. reading R for data science, will definitely help you follow this analysis.

Installation

It should be as simple as running the following:

# install.packages('remotes') # only if devtools isn't already installed
remotes::install_github('nimwegenLab/vngMoM')

Note that to analyse data obtained from Legacy MoMA, one should use the v0.1 branch of this package:

remotes::install_github('nimwegenLab/vngMoM', "v0.1")

Usage

This repository contains an example project, which can be used as a template for new projects, and also illustrate useful features of vngMoM.

Detailed information about the usage of vngMoM is provided in the readme file of example.

Contribution

In case you're granted read-only access to https://github.com/nimwegenLab/vngMoM repository, the recommend use is the following:

• fork this repository in your own account (it will be kept private even if you use a free github plan; by the way, you can get 5 private repositories for free at https://education.github.com/discount_requests/new).
• clone your repository (e.g. https://github.com/myAccount/vngMoM) to your local computer:
  git clone https://github.com/myAccount/vngMoM.git
• add https://github.com/nimwegenLab/vngMoM as a new remote to your local repository, calling it vng:
  git remote add vng https://github.com/nimwegenLab/vngMoM.git
• you can now pull from the nimwegenLab/vngMoM repository and push to yours if you want to update it / share new code:
  git pull vng master
git pull vng dev (if you want to pull the dev branch)
  git push origin master (or git push if you're lazy)
• after pushing your changes to your local repository (using an up-to-date version of nimwegenLab/vngMoM), you can create a pull request in the github web interface.
• (optionnal, and discouraged!) if you want to pull from vng and push to origin by default, you can change the git config locally:
  git config --local branch.master.remote vng (set vng as default remote)
  git config --local branch.master.pushremote origin (override the default push remote)