endoGenes- Reference Genes Analysis

This pipeline performs an automated analysis of the three most used algorithms to verify the stability of reference genes

STEP.1 -Download this repository to a preference path:

# Cloning the whole repository (Git is required)
# Open the terminal on unixOS and navigate to your work directory
 $ git clone https://github.com/hanielcedraz/endoGenes.git
 $ cd endoGenes
 $ chmod +x endoGenes.R

# Downloading zip file
   - Under the repository name, click in Clone or download.
   - Click on Download ZIP

STEP.2 - Install R

Access https://cran.r-project.org

Required files:

dataset file (default: endogenous_ct.txt)
efficiency list (default: efficiencies_list.txt)

#The amplification efficiency (2 = 100%). efficiency_values = E+1.

Usage on linux or Mac OS terminal:

$ ./endoGenes.R -f dataset_file.txt -e efficiency_list.txt

For those who do not use linux or macOS

Google Colab: https://github.com/hanielcedraz/endoGenes/blob/master/run_endoGenes_notebook.ipynb

ShinyApp: https://hanielcedraz.shinyapps.io/endoGenes/

Results

Tables

Bestkeeper

Genorm

NormFinder

Final Ranking

Plots