Connect with us

Software

GIANT: A New Tool for Transcriptomic Data Analysis

Tariq Abdullah

Published

on

Transcriptomic data analysis

Transcriptomic data analysis is an important requirement in biomedical research. The bioinformatics tools available for transcriptomic data analysis provide a user-friendly interface that is easily accessible by the experimental biologists as well. A new tool called GIANT-Galaxy-based tool for Interactive ANalysis of Transcriptomic data has been developed by Vandel et al., [1].

GIANT is a set of tools allowing researchers to analyze transcriptomic data from microarray or RNA-seq analyses [1]. It consists of different modules facilitating the easy selection of tools for a particular analysis. The source code of the GIANT is freely downloadable on Github (https://github.com/juliechevalier/GIANT). The Galaxy tool suite is available on the Galaxy Main Tool Shed (https://toolshed.g2.bx.psu.edu; name:suite_giant; owner:vandelj).

How GIANT works?

GIANT takes raw data from microarray or RNA-seq. Depending upon that, it selects methodology to process the data.

  • Firstly, it subjects the input data to a quality check.
  • In the next step, it leads to normalization including differential analysis in both the cases (microarray and RNA-seq).
  • After differential analysis, the data is subjected to another quality check. It is highly recommended [1].
  • After that, it generates volcano plots and heatmaps, performs clustering and GSEA formatting as per the user requirements.

GIANT suite consists of various adjustable parameters to improve the analysis and visualization of transcriptomic data. As an output, it provides interactive plots, tabular results, and easy visualization and sharing of the data. For further reading, click here.


References

  1. Vandel, J., Gheeraert, C., Staels, B., Eeckhoute, J., Lefebvre, P., & Dubois-Chevalier, J. (2020). GIANT: Galaxy-based tool for Interactive ANalysis of Transcriptomic data. Scientific Reports.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Software

SAUTE- New assembler for sequence assembly using target enrichment

Tariq Abdullah

Published

on

SAUTE- New assembler for sequence assembly using target enrichment

A new assembler called SAUTE is developed for sequence assembly that is based on target enrichment [1]. (more…)

Continue Reading

Docking

How to perform metal ion-protein docking using idock?

Dr. Muniba Faiza

Published

on

How to perform metal ion-protein docking using idock?

Previously, we provided a tutorial on the installation of idock on Ubuntu (Linux). In this article, we are going to demonstrate the docking of a metal ion (such as Zn, Mg, Fe, etc.,) with a protein using idock. (more…)

Continue Reading

Docking

How to install idock on Ubuntu?

Dr. Muniba Faiza

Published

on

How to install idock on Ubuntu?

idock [1] is a multithreaded software based on Autodock Vina. It is a virtual screening tool for flexible ligand docking. It also supports 27 different chemical elements including zinc, magnesium, iron, calcium, etc. In this article, we are going to install idock on Ubuntu. (more…)

Continue Reading

LATEST ISSUE

ADVERT