The full data analysis can be viewed as html:

htqpcr_ngs_comparison_R.html

In order to run the Jupyter notebook and to download the complete data set, please follow the instructions below.

Linux/Mac:

Clone repository

	$ git clone --recurse-submodules https://github.com/biologger/htqpcr_ngs_data

	# or alternatively
	$ git clone https://github.com/biologger/htqpcr_ngs_data.git
	$ git submodule init
	$ git submodule update

Install all dependencies with Anaconda or Miniconda

	$ conda env create -f conda_analysis_env.yml

Activate environment

	$ conda activate htqpcr_ngs_comparison

Start Jupyter Notebook

	$ jupyter-notebook

Open and Run the notebook

• htqpcr_ngs_comparison_R.ipynb

Windows:

We recommend a linux docker container or a linux OS in a virtual machine. For Windows install R Studio and Rtools manually.