eFP-Seq-Browser

The eFP-Seq Browser is an RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with an "electronic fluorescent pictographic" (eFP) image. This web-tool also allows the generation of new datasets if provided with SAM/BAM (with their index files) to allow visualization of any RNA-Seq mapping coverage. Gene expression levels and the similarity is also shown by calculating the Reads per Kilobase per Million reads mapped (RPKM) expression levels and Point Biserial Correlation Coefficient (r_pb) scores amongst its different splice variants.

Official publication of the eFP-Seq Browser can be found at https://doi.org/10.1111/tpj.14468.

Getting Started

It is recommended that you use the web version available at https://bar.utoronto.ca/eFP-Seq_Browser/ but if you want to download and run the eFP-Seq Browser locally, it is possible though it may require an internet connection to reach our webservices and Araport's APIs.

Browser Compatibilities

Chrome	Firefox	Edge	Safari	Opera	Tor	Mobile
✔	✔	✔	✔	✔	✔	✔

Installation

Clone the repository with git by running the following command:

git clone https://github.com/BioAnalyticResource/eFP-Seq-Browser.git

You will need Node.js and Python3 installed on your system to run the eFP-Seq Browser locally.

To set-up and install the prerequisites, run the following commands:

npm run install:all

which will install all the necessary Node and Python dependencies for the eFP-Seq Browser.

Running locally

To run the eFP-Seq Browser locally, once all packages are installed, simply run the following command and open your browser to http://localhost:3030/:

npm run start

This command will spin up two servers, one for the front-end and one for the back-end. The front-end server will be running on port 3030 and the back-end server will be running on port 3040.

Note

If you are running the backend Python scripts, because we are using CGI, you may want to run this in a Linux environment or modify the following files to get them working on your system: get_gene_structures.cgi and rnaSeqMapCoverage.cgi

Troubleshooting

Python3 not found

If you are using python instead of python3 as your Python executable, you can modify the start:backend script in package.json to use python instead of python3.

Validation

To run and test the eFP-Seq Browser code, you can run the following command:

npm run validate

Which will run the following commands:

• Prettier to format the code (npm run prettier)

Known issues

We aim to make the eFP-Seq Browser as perfect as possible but unfortunately, there may be some unforeseen bugs. If you manage to find one that is not here, feel free to create a bug report so we can fix it.

Current known issues:

• The IGB links do not work with Google Drive repositories
• If the web service timeouts, the eFP-Seq Browser will load continuously

Contributing

Please read CONTRIBUTING.md for more details.

License

SVG images are CC-BY SA 4.0. For rest: GPL-2.0

Authors

• Alexander Sullivan - GitHub, Twitter, ORCiD, LinkedIn, Website
• Priyank Purohit - GitHub
• Nowlan H. Freese
• Asher Pasha - Github, Twitter, ORCiD
• Eddi Esteban - ORCiD
• Jamie Waese - GitHub, Twitter, Website
• Alison Wu
• Michelle Chen
• Chih Ying Chin
• Richard Song
• Sneha Ramesh Watharkar
• Agnes P. Chan
• Vivek Krishnakumar
• Matthew W. Vaughn
• Chris Town
• Ann E. Loraine - Twitter, Website
• Nicholas J. Provart - Github, Twitter, Website