R-notebook-amino-acids

Data and analysis pipelines for amino acid supplementation experiments in Synechocystis.

Overview

This repository contains data from the analysis of a CRISPRi repression library. The experiments were carried out in the model cyanobacterium Synechocystis sp. PCC 6803. The repository contains raw data, processed data and R notebooks (*.Rmd) for next generation sequencing (NGS) of CRISPRi repression mutants.

All care was taken to adhere to good scientific practice in terms of statistics, reproducibility and code documentation. Please report any errors by filing a github issue for this repository, or contact michael.jahn@scilifelab.se.

Contents

• data - directory containing the input and output data
• docs- rendered pipeline in html format
  • Investigation of the effect of amino acid supplementation on fitness
• figures - exported figures from pipelines
• pipeline - data processing pipelines, R markdown format (.Rmd)

How to run the pipeline(s)

The pipelines 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. Pipelines can be downloaded and executed from the pipeline sub-folders. To simply view the rendered pipelines follow the links to the *.html reports at 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-notebook-amino-acids

Open 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")