elte_catmaid_course_25

Repo for ELTE Catmaid connectome analysis course - 2025 Jan

https://github.com/jekelylab/elte_catmaid_course_25

Repository

Repo for ELTE Catmaid connectome analysis course - 2025 Jan

README.Rmd

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
# Please put your title here to include it in the file below.
Title <- "Title of your paper goes here"
```


# An R project template to write scientific manuscripts reproducibly by integrating data, code, text and citations

About the project: 
- this is a template repository with an R project that the [Jékely lab](https://www.cos.uni-heidelberg.de/en/research-groups/gaspar-jekely) uses to start to write new research papers.

Add the specific information about your paper here:

This repository contains the data and code for our paper:

> Authors, (YYYY). _`r Title`_. Name of journal/book 

Our pre-print is online here:

> Authors, (YYYY). _`r Title`_. Name of journal/book, Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at 


### How to cite

Please cite this compendium as:

> Authors, (`r format(Sys.Date(), "%Y")`). _Compendium of R code and data for `r Title`_. Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at 

## Contents

The project directory contains:

  - [:file\_folder: text](manuscript/Manuscript.qmd): Quarto source document
    for manuscript. Includes text, references and inserts the latest version of the figures from the /figures folder. 
There is also a rendered html version,
    `Manuscript.html`, suitable for reading.
    
  - [:file\_folder: data](analysis/data): Data used in the analysis.
  - [:file\_folder: figures](manuscript/figures): Plots and other
    illustrations
  - [:file\_folder:
    supplements](manuscript/supplements):
    Supplementary materials including notes and other documents
    prepared and collected during the analysis.
  - [:file\_folder:
    source_data](manuscript/source_data):
    Source data files associated with each figure containing all data points that have been plotted in the figure. These files should be submitted together with the paper.

## How to run in your browser or download and run locally

This research compendium has been developed using the statistical programming
language R. To work with the compendium, you will need
installed on your computer the [R software](https://cloud.r-project.org/)
itself and optionally [RStudio Desktop](https://rstudio.com/products/rstudio/download/).

If you would like to use the template, you could open Rstudio in your computer, then go to File > New Project > Version Control > Git. Under repository URL add the URL of this page https://github.com/JekelyLab/new_paper_template and save it in a local folder.

The R project will live in the folder (as working directory) where the new_paper_template.Rproj file is saved. All other files and directories will be accessed relative to this working directory. This way the project is portable and self-contained.

The working directory contains this README file, a LICENCE file, a CITATION.cff file, the .gitignore file and the R project file. You can update these files to fit your project.

### Licenses

**Text, figures, code, data :**  [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)

### Acknowledgements

This project is modified after
https://annakrystalli.me/rrresearch/10_compendium.html.

Owner

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  Code documentation for my paper
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: John
    family-names: X
    orcid: 'https://orcid.org/0000-0000-0000-0000'
  - given-names: Jane
    family-names: Y
    orcid: 'https://orcid.org/0000-0000-0000-0001'
  - given-names: other
    family-names: authors
    orcid: 'https://orcid.org/0000-0000----'
identifiers:
  - type: doi
    value: add.the.zenodo.repository.doi
repository-code: 'https://github.com/add_github_link'
license: CC-BY-4.0
date-released: '2024-02-14'

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