GATTACA

GATTACA is a short for General Algorithm for The Transcriptional Analysis by one-Channel Arrays. It allows for an easy, painless and reproducible analysis of Differentially Expressed genes by using Microarray data.

GATTACA assumes data to be already background-subtracted, log2-transformed, and interarray-normalized. To this purpose, it provides methods to prepare data from raw files given by microarray scanners (see the Usage section below).

The available docker containers live on Docker Hub.

Disclaimer: These instructions are given with a unix-like environment in mind. The program was developed and tested in a Linux installation. See issue #3.

Installation

These scripts are bundled with their dependencies in a Docker container to make usage as painless and reproducible as possible. To install, follow these instructions:

1. Install docker. A tutorial can be found at the official docker website.
2. Get the GATTACA script. For example, you could run:

   curl https://raw.githubusercontent.com/Feat-FeAR/GATTACA/main/GATTACA --create-dirs -o ~/bin/GATTACA && chmod +x ~/bin/GATTACA

3. Run GATTACA -h to begin. The GATTACA script is the access point to all the other scripts in the repo. Read the usage section in this readme to learn more. The script takes care of downloading the containers and running them.

Troubleshooting

We tried to make the error messages given by GATTACA human-readable, so most issues should be solvable by reading the error message and consulting the manual. To ask for further help, open an issue.

Usage

Using the scripts is as simple as starting the GATTACA bash script. The various help messages (accessed using -h) detail the usage of each subcommand.

These are the currently available subcommands:

• GATTACA init: Used to create configuration files for GATTACA run.
• GATTACA run: Runs differential expression analysis on expression data.
• GATTACA annotate: Annotates expression data created by other commands with annotations from a variety of bioconductor packages.
• GATTACA prepaffy: Generates expression matrices from a collection of Affymetrix .CEL files.
• GATTACA prepagil: Generates expression matrices from a collection of Agilent .txt files.

The full GATTACA manual, which covers installation, usage and result interpretation can be downloaded here, from this repository, inside the /docs folder.

Building the image

If you wish to rebuild the Docker container, simply clone the repo, and run docker build .. More information on the docker build documentation page. Note that rebuilding the image can take a long, long time due to the need to install required packages (that need to be compiled).

Contributing

We welcome all contributions. Please read the contributing guide to learn more.