In hbc/hbcABC: Rmarkdown templates for bioinformatic analysis

This repository is for internal use, so any kind of script or template will be helpful to others. They don't need to be a final product, so go ahead and add anything you did that we don't have automatized.

R scripts

Scripts are being stored in inst/rmarkdown/Rscripts:

• Create a folder that categorize the analysis if it is not there.
• Create a R file that contains your code
• If you add the first line with a description: # this is for alternative splicing with IRFinder, it will be used as a description of the script in the page where all templates/scripts are being listed.

Rmarkdown

How to add new templates to HBC repository in 30 lines.

First you need to clone hbcABC repo to your computer.

After that, the easiest way to create templates is to follow this structure.

Inside the folder inst/rmarkdown/templates create a folder with the name of the RMD template you want to add, for instance: hello_word_rmd.

Then, create a YAML file named template.yaml with the following information:

name: Name of the template
description: >
  Description that will be shown in Rstudio.
create_dir: false

Create another folder named: skeleton and inside this a RMD file named skeleton.Rmd containing the rmarkdown you want to add.

At the end you'll should have this folders tree under inst/rmarkdown:

templates
-- hello_world_rmd
---- template.yaml
---- skeleton
------- skeleton.Rmd

To test it, install the package and go to the File -> New File -> R Markdown and click on templates. Your new template should be there.

hbc/hbcABC documentation built on Sept. 5, 2019, 9:51 p.m.