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ARMOR workflow

This is a graph of the ARMOR (Automated Reproducible MOdular RNA-seq) workflow. It shows all the steps in the workflow: Blue circles are rules run in R, orange circles from software called as shell commands. Dashed lines and light-colored circles are optional rules, controlled in config.yaml.

Using the ARMOR workflow

To use the ARMOR workflow on your own data, follow the steps outlined below carefully.

1. Clone this repository to your local machine and set the working directory to the cloned repository:

   git clone https://github.com/csoneson/ARMOR.git
   cd ARMOR
   

2. Prepare the input files (FASTQ files and a metadata file)

3. Make sure that all the necessary software is available. This can be done in two ways:

   a. Set up and activate a conda environment

   b. Install software manually

4. Prepare the configuration file (config.yaml)

5. Set up the proper experimental design and contrast(s) for differential expression analysis

6. Run the analysis

7. Visualizing results with iSEE

Testing the setup

We provide a small example data set that you can use to test your setup: See Testing the setup.

Interactive R sessions

Note that this repository includes an .Renviron file which is used to automatically configure R on startup. This is useful when you have an active conda environment and you want to explore your data in an interactive R session (started in the ARMOR directory). The .Renviron file removes any user specific library paths on startup, ensuring that you will only have access to R packages that are installed in the active conda environment.