R markdown notebooks to document my computational biology projects. This repository contains data processing pipelines or data curation projects that require a higher level of maintenance and documentation.
In contrast to some of my other github projects, like SysbioTreemaps, ShinyMC, ShinyProt, or ShinyLib, the pipelines in this repository are not necessarily in the form of R packages or apps. This means the pipelines were created for a particular purpose or data analysis task, but are not further developed or maintained.
The pipelines and their documentation collected here therefore come with no warranty regarding stability or runability in future R versions. However, all care was taken to guarantee scientific accuracy and adhere to good scientific practice in terms of statistics, reproducibility and code documentation. Please report any errors by filing a github issue.
The pipelines collected in this repository are self-contained and executable.
The code and the documentation are part of one and the same R markdown document
for each pipeline. The pipelines themselves can be downloaded and executed
from the pipeline sub-folders. To simply view the rendered pipelines follow
the links to the *.html reports under Contents.
To download the repository on your local drive use git clone in a (linux) terminal:
cd /your-target-folder
git clone https://github.com/m-jahn/R-notebooks.gitOpen a pipeline with Rstudio and execute code (chunks) with the Run button.
Alternatively, open an interactive R session and render the R markdown pipeline:
require(rmarkdown)
rmarkdown::render("pipeline.Rmd")