BioC2024

Transcriptomic profiling became a standard approach to quantify a cell state, which led to accumulation of huge amounts of public gene expression datasets. However, reuse of these datasets is inhibited by the lack of uniform format of how such data is deposited. This leads to the situation when actually getting the data ready for analysis requires many steps such as loading the gene expression values, feature and sample annotation, normalization, quality check and outlier filtering. Here we present Phantasus – a user-friendly web application for interactive gene expression analysis which provides streamlined access to almost 120,000 public gene expression datasets from Gene Expression Omnibus. Importantly, Phantasus supports both public microarray and RNA-seq datasets as quantified by ARCHS4 and DEE2 projects. With Phantasus, researchers can quickly and easily perform quality checks and analysis through its intuitive and highly interactive JavaScript user interface integrated with opencpu-based R backend. Phantasus is available at https://alserglab.wustl.edu/phantasus as well as the Bioconductor R package (https://bioconductor.org/packages/phantasus). We further provide a lightweight phantasusLite package (https://bioconductor.org/packages/devel/bioc/html/phantasusLite.html) featuring helper R functions for working with public datasets, in particular providing an access for RNA-seq counts stored at the remote HSDS (Highly Scalable Data Service) server.