https://github.com/jasenfinch/spectral_binning_as_an_approach_to_post-acquisition_processing_of_fie-hrms_data

Spectral binning as an approach to post-acquisition processing of high resolution FIE-HRMS metabolome fingerprinting data
https://github.com/jasenfinch/spectral_binning_as_an_approach_to_post-acquisition_processing_of_fie-hrms_data

manuscript mass-spectrometry metabolomic-fingerprinting metabolomics post-acquisition-processing reproducible-research

Last synced: 4 days ago
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Spectral binning as an approach to post-acquisition processing of high resolution FIE-HRMS metabolome fingerprinting data

• Host: GitHub
• URL: https://github.com/jasenfinch/spectral_binning_as_an_approach_to_post-acquisition_processing_of_fie-hrms_data
• Owner: jasenfinch
• License: cc-by-4.0
• Created: 2022-02-09T21:50:18.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2022-08-18T10:46:00.000Z (over 2 years ago)
• Last Synced: 2024-01-27T08:03:24.320Z (11 months ago)
• Topics: manuscript, mass-spectrometry, metabolomic-fingerprinting, metabolomics, post-acquisition-processing, reproducible-research
• Language: R
• Homepage: https://doi.org/10.1007/s11306-022-01923-6
• Size: 71.3 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# Spectral binning as an approach to post-acquisition processing of high resolution FIE-MS metabolome fingerprinting data

[![Docker](https://github.com/jasenfinch/Spectral_binning_as_an_approach_to_post-acquisition_processing_of_FIE-HRMS_data/actions/workflows/dockerpublish.yml/badge.svg)](https://github.com/jasenfinch/Spectral_binning_as_an_approach_to_post-acquisition_processing_of_FIE-HRMS_data/actions/workflows/dockerpublish.yml)

[![License: CC BY 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)

This is the code and analysis repository for the article:

[Finch, J.P., Wilson, T., Lyons, L., Phillips, H., Beckmann, M. and Draper, J., 2022. Spectral binning as an approach to post-acquisition processing of high resolution FIE-MS metabolome fingerprinting data. *Metabolomics*, 18(8), pp.1-9.](https://doi.org/10.1007/s11306-022-01923-6)

All code is written in R and the [drake](https://docs.ropensci.org/drake/) package has been used for workflow management.

The [renv](https://github.com/rstudio/renv) package has been used to ensure a reproducible R environment.

## Compile the manuscript

### Using docker

The manuscript can be compiled using a pre-built docker image, directly from GitHub:

``` sh

docker run -v $(pwd):/home/rstudio/Spectral_binning_as_an_approach_to_post-acquisition_processing_of_FIE-HRMS_data ghcr.io/jasenfinch/spectral-binning:latest

```

### Locally

To generate the manuscript, simply [clone the repository](https://git-scm.com/book/en/v2/Git-Basics-Getting-a-Git-Repository), open the R console, set the working directory to the repository clone using `setwd()` and run the command `drake::r_make()`.