Core Concepts
Phantasus is a user-friendly web application that integrates an intuitive JavaScript-based heatmap interface with powerful R-based analysis methods, enabling seamless gene expression analysis from data loading to downstream insights.
Abstract
Phantasus is a web application developed for interactive gene expression analysis. It combines a JavaScript-based heatmap interface with an R-backend to provide a comprehensive analysis pipeline. Key features include:
Data Loading: Phantasus supports loading gene expression data from various sources, including direct access to over 84,000 public datasets from the Gene Expression Omnibus (GEO) database.
Data Preprocessing: The application offers tools for data normalization, filtering, and aggregation, allowing users to perform thorough quality control and prepare the data for downstream analysis.
Exploratory Analysis: Phantasus provides interactive visualization and analysis methods, such as principal component analysis, clustering, and sample/gene profiles, to help users explore the data and identify patterns.
Differential Expression: The application integrates R-based differential gene expression analysis using limma and DESeq2, enabling users to identify genes with significant changes between sample groups.
Downstream Analysis: Phantasus seamlessly integrates with external tools like Enrichr and Shiny GAM for pathway enrichment and metabolic network analysis, allowing users to gain deeper biological insights.
Interactivity and Sharing: The JavaScript-based interface offers a highly interactive experience, allowing users to manipulate data, annotations, and visualizations directly in the web browser. Phantasus also supports session sharing, enabling collaborative work and publication-ready data presentations.
Deployment Options: Phantasus can be accessed online through official mirrors or installed locally as an R package or Docker image, providing flexibility for users.
Overall, Phantasus aims to simplify the gene expression analysis workflow by integrating an intuitive user interface with powerful R-based computational methods, making it accessible to both domain experts and users with limited programming experience.
Stats
Phantasus provides access to over 84,379 gene expression datasets from the Gene Expression Omnibus (GEO) database.
Phantasus supports 49,666 microarray datasets based on 2,767 platforms, with 39,689 datasets having machine-readable annotations.
The RNA-seq dataset subset consists of 34,713 datasets, with data sourced from the ARCHS4 and DEE2 databases.
Quotes
"Phantasus integrates an intuitive and highly interactive JavaScript-based heatmap interface with an ability to run sophisticated R-based analysis methods."
"Phantasus allows to go all the way from loading, normalizing and filtering data to doing differential gene expression and downstream analysis."