Top 5 of the Best Free Tools to Visualize Your Transcriptome Data

It is not always easy to illustrate the data you create when you study transcriptomics. Therefore it is not easy to make sense of all this data, either to analyze it or to communicate with your colleagues. Maybe you need a tool to bring your data from raw to “enjoyable” and “meaningful”?

Data visualization responds to two major challenges, the first one is communication. Using the right tool to exhibit your data to the community is primordial. It will show the sense of data at a glance.

The other challenge data visualization responds to is understanding. The data visualization tools enable to organize your data. It helps to get the message out there.

Let’s see in details our top 5 of European web-based transcriptomics data visualization tools. The cherry on top: they are all free to use.

MLCut

Online tool • For life sciences • Made in the UK • Free

The Edinburgh Napier University calls MLCut a “tool that provides visual support for exploring dendrograms of heterogeneous data sets in different levels of detail” in the Computer Graphics & Visual Computing journal.

It allows an effective dendrogram representation that scales well for large data sets.

MLCut offers the ability to explore, in different levels of detail, the dendrogram and the representation of the original data.

You can view the whole data set and select some of the clusters on display during the exploration process. And you can easily export selected clusters for further analysis.

Here are some of the cluster representations you can have in MLCut from the same article in the Computer Graphics & Visual Computing journal.

Listeriomics

Online tool • For life sciences • Made in France • Free

Listeriomics is a tool from the Pasteur Institute which integrates the complete genomes, transcriptomes, and proteomes for Listeria species published to date.

You can browse RNA-Seq and tiling arrays of a specific strain of _Listeria monocytogenes_in a different medium, temperature, and phase. And you can choose the criteria you want in this list for example:

You can then visualize RNA sequencing data in the condition you chose like this:

It is a well-adapted tool to decipher the regulatory mechanisms of a selected element of the genome.

ExpVIP

Online tool • For life sciences • Made in the UK • Free

ExpVIP is a visualization platform that allows integration of your data visualization (graphs, calculated data) into your files.

It is an intuitive and interactive interface that allows easy analysis of RNA-seq data.

The open-access expVIP platform aims at facilitating the analysis of gene expression data from a wide variety of species. It allows the easy integration, visualization, and comparison of RNA-seq data across experiments.

It generates a custom Web browser to visualize, sort, and filter the RNA-seq data. It also provides outputs for differential gene expression analysis.

Here is an illustration of the implementation of expVIP, extracted from an article of the journal Plant Physiology:

With expVIP, users can analyze public and user-specified data sets with minimal bioinformatics knowledge.

Here is an example of gene expression visualization with expVIP:

BioJS

Online tool • For life sciences • Made in the UK • Free

BioJS is open-source and community-driven. As the BioJS website claims, “basically BioJS components behave like Lego blocks”. You can build on top of other blocks.

In fact, BioJS is a “building block” that can be reused whenever you need it. It can be a tree algorithm or a simple visualization module.

BioJS is a library of over a hundred JavaScript components enabling you to visualize and process data. It gathered the 191 components (at this date) in the BioJS Registry. You can create your own JavaScript component tailored to your data.

The library offers a wide range of components. And if you don’t find what you are looking for, you have the possibility to create your own tailored BioJS component.

Here is a video to explain what you can achieve this with BioJS:

EMAGE

Online tool • For life sciences • Made in the UK • Free

EMAGE is the eMouse Atlas of Gene Expression. It is an online resource that publishes the results of in situ gene expression experiments on the developmental mouse.

It allows data interrogation by what is called “spatial methods”. The principle is to spatially integrate domains of expression from raw data images into a set of standard 3D virtual mouse embryos at different stages of development.

You can see this manual spatial mapping feature here, extracted from an article on EMAGE of the Nucleic Acids Research journal.