/eFP-Seq-Browser

An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.

Primary LanguageHTMLGNU General Public License v3.0GPL-3.0

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 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 Pearson Correlation Coefficient (PCC) scores amongst its different splice variants.

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 webservers and Araport's APIs.

Browser Compatibilities

Chrome Firefox IE Edge Safari Opera
✔ ✔ X ✔ ✔ ✔

Installation/Open

If you wish to modify the code, all .CGI files use Python 2 as well as there are a few Perl scripts. If you are running the primary webservice (rnaSeqMapCoverage.cgi) locally, you will also need to install SAMTools.

Outside of that, there is nothing to install, just download all the files and open "index.html" (legacy.html is no longer supported).

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.

  • After generating a new dataset through the "Generate Data" option, the user cannot scroll up without first scrolling down
  • The IGB links do not work with Google Drive repositories
  • Download page as an image does not render SVGs in Microsoft Edge

Contributing

Please read CONTRIBUTING.md for more details.

License

SVG images are CC-BY SA 4.0. For rest: GPL-3.0

Authors