Prepare for manuscript submission

.Rprofile

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+source("renv/activate.R")

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+
+# Ignore data and manuscript folder
+data/*
+manuscript/*
+
+# Renv
+renv/library/*
+renv/staging/*

CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this code, please cite it as below."
+authors:
+  - family-names: Leegwater
+    given-names: Hanneke
+    orcid: https://orcid.org/0000-0001-6003-1544
+title: "Normalization strategies for lipidome data in cell line panels"
+version: 1.0.0
+date-released: 2024-02-08

LICENSE

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+MIT License
+
+Copyright (c) 2024 Hanneke Leegwater
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Lipidomics.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

README.md

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-# Leegwater_lipidomics_normalization
+# Leegwater - Normalization strategies for lipidome data in cell line panels
+
 Code and example dataset to generate figures for "Normalization strategies for lipidome data in cell line panels" (Leegwater et al. submitted)
+
+## Usage
+
+Within the code folder, you will find two R markdown files and a functions folder. The R markdown files can be used to rerun all code and to create all figures. Functions that one might want to reuse can be found in the functions folder. 
+
+### Data
+
+Metabolomics data have been deposited to the EMBL-EBI MetaboLights ([`Yurekten et al., 2024`](https://doi.org/10.1093/nar/gkad1045)) with the identifier MTBLS9493and is accessible at https://www.ebi.ac.uk/metabolights/MTBLS9493. 
+
+When this dataset status is changed to public, we will add it and metadata to the data folder in this repository. For now, you can take a look at the html reports to see what the data could look like.
+
+### Figures
+
+Figures are generated reproducibly in R using [`renv`](https://rstudio.github.io/renv/index.html):
+
+1.  Download/clone this repository
+
+2.  Open the project file (`.Rproj`) in RStudio
+
+3.  Run
+
+    ``` r
+    renv::restore()
+    ```
+
+    to install R package dependencies.
+
+4.  Open `code/Calculations_to_get_all_data_for_all_figures.Rmd` and choose *Run* \> *Run All*. You may need to set a custom directory for the data, since this is not yet part of this repository.
+
+5.  Open `code/All_figures.Rmd` and choose *Run* \> *Run All*. Figures will appear in the specified `output_dir` folder.
+
+## Acknowledgments
+
+Thanks to [@burgerga](https://www.github.com/burgerga) for suggestions on archiving this repository.