The rise of modern gene expression profiling techniques, such as bulk RNA sequencing, has generated a wealth of high-quality datasets spanning all fields of current biological research.
Bulk RNA-Seq is the method of choice for transcriptomic analysis of pooled cell populations, tissue sections, or biopsies.
It measures the average expression level of individual genes across hundreds to millions of input cells and is useful for getting a global idea of gene expression differences between samples. The downstream analysis results can be visualized using many plots like PCA, volcano plots, heatmaps, scatter plots, box plots, etc.
In this blog, we will compare a few features of different web-based applications used to visualize bulk RNA-Seq data.
There are 3 main challenges in visualizing bulk RNA-Seq data.
Widely Used Bulk RNA-seq Data Visualization Tools
Let’s look at a few of the most popular web-based tools for visualizing bulk RNA-sequencing data.
Although bulk RNA-Seq has prevailed as the major technique for studying genome-wide gene expression profiles, the user communities are still struggling to create gold standards encompassing all related data analytics stages. While the data generation and analysis steps are well-defined and tools for each step are generally mature, there is a lack of integrated solutions covering most of them, from data management and genome browsing to biologically relevant outcomes. Users must look for web-based or stand-alone applications for downstream analysis and visualization.
However, Phantasus, a third-party application on Polly, can expedite bulk RNA-Seq data processing because Polly offers the world's most extensive collection of well-curated ML-ready bulk RNA-Seq data. These datasets have been metadata harmonized, which makes the bulk RNA-seq data visualization and analysis process smoother. The input file (.GCT format) is accessible for various publicly available data sets on our platform. Researchers can use Phantaus on the Polly platform with either a graphical user interface or a programmatic interface to access, view, and study these carefully maintained datasets.
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