Workshop rspacer

Materials and instructions for workshops on using rspacer together with RSpace and LACDR-ISA templates.

These tutorials demonstrate how R can be used to generate structured reports and automatically upload these to an RSpace electronic lab notebook (ELN).

Contributions and suggestions are welcome. Please open an issue or submit a pull request if you notice problems or have improvements.

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Feel free to help us improve these materials, we are very happy with any suggestions. You can reach us by either submitting an issue or directly fix a problem using a pull request.

Introduction

This repository contains materials and instructions for workshops on using rspacer and LACDR-ISA templates together with RSpace.

At the point of writing, the workshops are step by step guides with example documents, and are meant as LACDR-specific extensions to the tutorials on the rspacer website, and instructions on the LACDR-ISA package page.

You can also find our preprint here

Links to tutorials

• Tutorial 1
• Tutorial 2
• Tutorial 3
• Tutorial 4
• Installation instructions

Tutorial details

Tutorial 1 - Using R Projects

After this tutorial, you will be able to:

• Explain how an R project can make your research more reproducible
• Set up your own R project in RStudio

Tutorial 2 - Using LACDR-ISA Quarto and Excel templates

After this tutorial, you will be able to:

• Explain the benefits of using structured templates
• Apply the Investigation-Study-Assay (ISA) structure to your own research projects
• Use LACDR-ISA Templates in both RStudio and Excel
• Adapt the LACDR-ISA Templates to your own research needs

Tutorial 3 - Document from HTML

After this tutorial, you will be able to:

• Generate a Quarto report
• Upload a rendered Quarto HTML report as an RSpace Document using rspacer.

Tutorial 4 - Document from Excel

After this tutorial, you will be able to:

• Upload information from Excel, CSV or TSV files to specific fields in an RSpace Document using rspacer.

Tutorials to be written

Tutorial 5 - Reusing data from RSpace

After this tutorial, you will be able to:

• Download metadata from RSpace using rspacer
• Reuse stored metadata in R
• Upload metadata to an RSpace lab journal entry

The functionality already exists, but we have not yet written the tutorial. For now, read the Help pages and the vignette of: rspacer::folder_tree, rspacer::document_list_attachments and rspacer::file_download.

Tutorial 6 - Add attachments to an existing document

After this tutorial, you will be able to:

• Upload files to RSpace from R using rspacer
• Attach files to an existing document using rspacer

Tutorial 7 - append information to an assay 1.

• For now, see our preprint and our website
• Use rspacer::document_append_from_html to get this done.

Installation instructions {#installation-instructions}

Requirements: you need to have R Studio and R installed, and you need an account on RSpace.

1. Clone or download this repository
2. Open the repository as an RStudio project
3. Navigate to a tutorial folder
4. Open the Tutorial_X.md file