Bulk RNA-Seq View is an easy-to-use system for bulk RNA-Seq data analysis and visualization.

Start Bulk RNA-Seq View

Easily process public or private bulk RNA-Seq data, set up the comparisons, identify changed genes and enriched pathways, and further visualize the results using interactive data mining tools.

FAQ

Bulk RNA View contains most updated collection of the human public bulk RNA-Seq data sets from GEO database. It also contains the pipeline to process the data sets, and easy-to-use tools to display the results in plots and tables, including sample relationship (PCA plot, heatmap), gene expression, DEGs and enriched pathways. The interactive plots can be easily customized to meet the publication requirement according to user’s preference.

Anyone who has basic knowledge of and is interested in the bulk RNA-seq data analysis. No coding experience is required.

Click on button Start Bulk RNA-Seq View, you will see a table listing all the available data sets. Find your interested data set first.

Check for the last Actions column, there are two links: Quick View and DEG Analysis.

To view the expression data, please click on the Quick View. You will enter the result display page. Try to select different sections in the top menu. Each section has several tabs of different tools. Help locates at the last tab containing the explanation of all the tools in every section.

To find the DEG and enriched pathways, please click on the DEG Analysis link in the last Actions column, and you will see the analysis setup page. The page shows the sample meta table, which can be used to create the comparisons of interest at the bottom of the page. If you want to make comparisons whose grouping information does not exist in the sample meta table, you can check the Edit the sample information link on the top of the page and follow the instructions to update the sample meta table. After you fill in all the comparison information, click on the Start Analysis button. After a few moments, you will see the very similar page as you can see in the Quick View. But in this page, you will see 3 more sections: DEGs, Gene Set Enrichment and Venn Diagram. These are the tools used to explore the comparison values.

scRNA View is an upcoming package that enables automatic single-cell RNA-Seq data analysis, coupled with powerful visualization. scRNA View integrates the single-cell database, CellDepot, which takes advantage of the data analysis visualization power from Cellxgene VIP.

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scRNA View consists of two components: a scRNAseq data process pipeline and data visualization platform. The pipeline provides highly automated computational analysis to speed up the turnaround time. The visualization platform enables users to access the gene expression results at single cell level from anywhere and make continuous discovery with a variety of user-friendly data mining tools for publication ready figures.

Contact Us for help on how to process scRNAseq data, or would like to upload your data to the online visualization tool.