Learning Outcomes

• Understand the functionality of the Report tab in the run page.
• Learn how to visualize output files with various applications.
• Discover available example applications for data analysis.

Visualizing Reports

The Report tab appears on the run page on run completion, allowing you to visualize output files using various applications and tools. Below is an example of a Report section from an RNA-Seq pipeline:

Each entry in the report corresponds to an output from the pipeline's workflow. To view the details of any entry, simply click on it. Additionally, each section features Download, Full Screen, and Open in New Window icons.

Integration of Custom Visualization Tools

To integrate your own visualization tool into Via Foundry, please review our App guide or contact us at support@viascientific.com. Our team will be happy to assist you.

Example Applications

Shiny App - DEBrowser

DEBrowser is an R library designed for simplifying the performance and visualization of Differential Expression (DE) analysis. This module accepts count matrices as input and enables interactive exploration of the output data. For more detailed information, refer to the DEBrowser Documentation.

R-Studio - R-Markdown

The R-Studio launcher supports the interactive analysis of data generated from your run. We provide a selection of R-Markdown reports, allowing immediate access to your report in HTML or PDF format upon completion of the run.

Here is an example code snippet for performing differential expression analysis on each comparison listed in the comparison file. This code generates volcano and MA plots for differentially expressed genes:

Jupyter Notebook

Jupyter Notebook provides bioinformatics researchers with the ability to seamlessly combine code, visualizations, and explanatory text in a single document. This interactive platform enables users to write and execute code snippets in real-time, visualize data using various plotting libraries, and document their analyses step-by-step.

Shiny App - GSEA Explorer

GSEA Explorer is an R library that offers a user-friendly platform to conduct and visualize Gene Set Enrichment Analysis (GSEA). GSEA assesses whether a specific gene set or pathway is enriched in gene expression data, aiding researchers in interpreting RNA-seq results and enhancing the understanding of biological mechanisms. Access GSEA Explorer after executing Foundry's complete RNA-sequencing pipeline or the standalone Differential Expression module.

Shiny App - Network Explorer

The Network Explorer application allows bioinformaticians to analyze complex networks, uncover hidden patterns, identify key players, and understand underlying biological mechanisms. You can launch Network Explorer after running Foundry's full RNA-sequencing pipeline or the standalone Differential Expression module.

Tables

Tables facilitate viewing, sorting, and searching through the csv/tsv file content. Below is an example illustrating feature count summaries:

To fit the entire table on your screen, click the Full Screen icon located at the top-right of the module.

HTML/PDF Viewer

The HTML/PDF Viewer allows seamless integration of HTML/PDF content into our Report section. An example of MultiQC output is illustrated below:

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