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https://github.com/jwist/fusion

Offer a data structure to manage metabolic profiling data for NMR and MS spectroscopy
https://github.com/jwist/fusion

metabolomics ms nmr

Last synced: 5 days ago
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Offer a data structure to manage metabolic profiling data for NMR and MS spectroscopy

Host: GitHub
URL: https://github.com/jwist/fusion
Owner: jwist
License: other
Created: 2020-11-25T05:23:19.000Z (almost 4 years ago)
Default Branch: master
Last Pushed: 2024-01-10T09:25:17.000Z (10 months ago)
Last Synced: 2024-01-10T10:35:24.988Z (10 months ago)
Topics: metabolomics, ms, nmr
Language: R
Homepage:
Size: 19.3 MB
Stars: 0
Watchers: 1
Forks: 2
Open Issues: 4
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

# fusion

[![Codecov test coverage](https://codecov.io/gh/jwist/fusion/branch/master/graph/badge.svg)](https://codecov.io/gh/jwist/fusion?branch=master)
[![Travis build status](https://travis-ci.com/jwist/fusion.svg?branch=master)](https://travis-ci.com/jwist/fusion)

Fusion aim at providing a structure to data produce for metabolic profiling or phenotyping using nuclear magnetic resonance and mass spectrometry.

## Pre-requisites

You will need to manually install two dependencies:

```r
remotes::install_url("https://anpc.mylims.org/gitea/jul/rldx/archive/main.tar.gz")

remotes::install_github("phenological/[email protected]")
```
## Installation

You can install the released version of fusion from github:

``` r
devtools::install_github("jwist/fusion")
```

### post-installation

ANPC members can perform some environment configuration by running the startup script provided here. Before, it is important to know the path of the institutional OneDrive Folder and to check that the datasets folder exists and is in sync.

It is also important to be able to locate the .Rprofile that allows users to perform task during R startup and the .Renviron file that allows to define variable to be used while starting R. Both files are usually located into the home directory of the user that runs the R instance.

``` r
homePath <- Sys.getenv("HOME") # locate your home directory
file.path(homePath, ".Rprofile") # typical location of .Rprofile
file.path(homePath, ".Renviron") # typical location of .Renviron

fusion::startup()
```

### Troubleshooting
- Both files are usually hidden by the windows manager of major OS. Check how to toggle the display of hidden files in your file browser.
- Make sure that you have the permission to read in the datasets folder.

## Introduction