Phantasus: visual and interactive gene expression analysis

This documentation describes Phantasus – a web tool designed for visual and interactive gene expression analysis. In particular, it was designed to allow to go from a typical dataset to differential expression and downstream analysis in an easy and streamlined manner. For that aim, Phantasus integrates an intuitive heatmap interface with gene expression analysis tools from Bioconductor.

Main features:

• Loading public datasets from Gene Expression Omnibus with both microarrays and RNA-seq datasets (via ARCHS4) being supported.
• Differential gene expression using limma or DESeq2.
• Publication ready plots with export to SVG: PCA plot, row profiles, box plots.
• Clustering: k-means and hierarchical.
• Gene set enrichment analysis via fgsea package.
• Sharing session links.

Links:

• Official mirror: https://alserglab.wustl.edu/phantasus.
• Source code at GitHub: https://github.com/ctlab/phantasus.
• Bioconductor package: https://bioconductor.org/packages/phantasus.
• Docker image: https://hub.docker.com/r/alserglab/phantasus.

Citation:

• Kleverov M, Zenkova D, Kamenev V, Sablina R, Artyomov M, Sergushichev A (2024). Phantasus, a web application for visual and interactive gene expression analysis. Elife, 13, e85722. https://doi.org/10.7554/eLife.85722