ugrbioinfo/ellba repository overview

⁠ELLBA (Ensemble Learning for Liquid Biopsy Analysis)

⁠What is ELLBA?

ELLBA is an established workflow for analyzing liquid biopsy-derived RNA sequencing (lbRNA-seq) data, tailored to address complexities in clinical settings. It encompasses six biologically motivated feature types: gene expression, isoform expression, FoCT, gene fusion, RNA editing, and SNVs, each providing diagnostic and prognostic value in diseases like cancer. ELLBA employs Ensemble Learning to combine these features, enhancing prediction accuracy and facilitating personalized cancer care.

⁠Getting started

The simplest approach to utilize ELLBA is through its Docker image.

The ELLBA Docker image offers users a self-contained environment equipped with all the necessary tools and dependencies, including REDItools2, STAR aligner, bcftools, etc., essential for lbRNA-Seq data analysis.

To get started, you'll need to have Docker installed on your system. Below are installation instructions for Ubuntu and MacOS:

For Ubuntu:

1. Docker installation

sudo apt update
sudo apt install docker.io

1. To start Docker as a service on Ubuntu

sudo systemctl start docker
sudo systemctl enable docker

To retrieve the ELLBA Docker image from DockerHub, you can use the following command:

sudo docker pull ugrbioinfo/ELLBA:latest

Once you've successfully downloaded the ELLBA Docker image, you can launch it with the following command:

sudo docker run --hostname ELLBA --name ELLBA --workdir /home/ellba -it ugrbioinfo/ellba:latest /bin/bash

Alternatively, if you prefer to initiate the container with shared folders, you can follow these step:

sudo docker run --hostname ELLBA --name ELLBA --workdir /home/ellba--mount type=bind,source=MACHINE_FOLDER,destination=/shared/shared_folder -it ugrbioinfo/ellba:latest /bin/bash

After your initial usage of the container, you can exit it by typing "exit." To stop the container entirely, you can use the following command:

sudo docker stop ELLBA

For subsequent usage, you can follow these steps:

sudo docker start ELLBA
sudo docker exec -term=SCREEN -it ELLBA /bin/bash