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This repository contains files to reproduce the heuristic evaluation environment described in the paper "Usability evaluation of circRNA identification tools: Development of a heuristic-based framework and analysis".

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Usability evaluation of circRNA tools

This repository contains files to reproduce the heuristic evaluation environment described in the paper "Usability evaluation of circRNA identification tools: Development of a heuristic-based framework and analysis". Link to article.

Contents

A small test dataset of Homo sapiens data is provided, including reference genome, annotation, one paired-ended library, and genome indexes (bowtie, bowtie2, bwa, STAR). Genome, annotation, and RNA-Seq data were originally obtained from CirComPara test data. We also provide support scripts to install some libraries and packages.

├── data  # Test dataset    
│   ├── annotation
│   ├── index
|   │   ├── bowtie
|   │   ├── bowtie2
|   │   ├── bwa
|   │   └── star
│   ├── reads
│   └── reference
│   
├── support   # support scripts

How to use

Install Docker according to your OS

Docker can be installed on multiple platforms. Please refer to the specific instructions on the official documentation.

Build the image

Download or clone this repository. After that, build the Docker image from the Dockerfile:

cd circrna-usability/
docker build -t usability-env .

Run a container

Create a new container to evaluate each tool.

docker run -v $(pwd):/circrna-usability -it usability-env bash

This command will create a container running an interactive shell in a Ubuntu 18.04 system. It will also map the circrna-usability folder on your host system to the circrna-usability folder inside the container. Any changes made inside this folder will reflect on both systems.

Perform the heuristic evaluation

Download and install a circRNA tool inside the container system. Perform your heuristic evaluation and fill the evaluation sheet.

Citation

Guilherme Bauer-Negrini, Guilherme Cordenonsi da Fonseca, Carmem Gottfried, Juliana Herbert. Usability evaluation of circRNA identification tools: Development of a heuristic-based framework and analysis. Computers in Biology and Medicine, 2022, 105785, ISSN 0010-4825, https://doi.org/10.1016/j.compbiomed.2022.105785.

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This repository contains files to reproduce the heuristic evaluation environment described in the paper "Usability evaluation of circRNA identification tools: Development of a heuristic-based framework and analysis".

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