ABioTrans Plus

A Biostatistical tool for Transcriptomics Analysis

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ABioTransPlus is a web server for transcriptome data analysis and visualization. It supports the analysis of microarray and RNASeq data and performs ten different bio-statistical analyses that cover the common analytics for gene expression data. Furthermore, it gives the users access to several bioinformatics tools to perform 12 different bioinformatics analyses on gene/protein datasets.

ABioTransPlus is designed as a one-stop server that helps the users perform all tasks through an intuitive graphical user interface (GUI) that waves the hassle of coding, installing tools, packages or libraries and dealing with operating systems compatibility and versioning issues, some of the complications that make data analysis tasks more challenging for biologists. ABioTrans Plus is an open-source tool and the website is free and open to all users and there is no login requirement.

ABioTransPlus is available at http://combio-sifbi.org/ABioTrans/

If you find ABioTrans useful, please cite our paper: Zou Y, Bui TT and Selvarajoo K (2019) ABioTrans: A Biostatistical Tool for Transcriptomics Analysis. Front. Genet. 10:499. doi: 10.3389/fgene.2019.00499

Full text (free access) can be found at https://www.frontiersin.org/articles/10.3389/fgene.2019.00499/full

Download instructions

  1. Scatter plot, distribution fit, correlation plot and heatmap can be saved as PDF by clicking Download as PDF. You can name the file before saving it. Also, you can directly drag the plot from the GUI to a folder on the computer.

  2. PCA, noise, entropy and gene ontology pie chart are supported by Plotly. If you are using the GUI in R window or Safari, click Download as PNG and it may take 5 seconds to save the graph. You cannot name the file yourself, so please be aware of overwriting issues. Even if the plot is saved successfully, there may be a 404 Not found message after downloading. Please go to your working directory and check. If you cannot save the graph successfully, please try the following code the Rstudio command line. You only need to run this code once. (You can also simply take a screenshot of the graph.)

webshot::install_phantomjs()

If you are using R window or Safari, and you cannot save PCA-3D graph successfully, please create a plotly account (free). Please go to this website on the instructions of creating a new account and Find your authentication API keys in your online settings (https://plot.ly/r/getting-started/). After that please go to the first two lines in ABioTrans.R file, remove both of the "#" signs, and replace the username and api key with your own. Save the file before you run. However, please be reminded that this Download as PNG button only downloads the PCA-3D plot from the default angle.

  1. For Chrome users, the Download as PNG button may be disabled. Please put your mouse over the graph region and click the left most camera sign to save the plot. It will be saved in the download folder on your computer. You are suggested to use Chrome because it saves you trouble from creating an account and changing the code. More importantly, you can download the PCA-3D plot from any angle.

Docker Support

Now we also have a docker image containing all the dependencies needed to run ABioTrans Plus. It also support shiny-server opensource which can be exposed in port 3838.

It can be pulled using docker pull jaktab/abiotrans-webserver:latest