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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
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Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...
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SeqExpressionAnalyser: An R Package for Automated End-to-End RNA-Seq Analysis From Reads to Differential Expression.

Sanae Esskhayry1,2,3, Ouafae Kaissi2, Fouzia Radouani4

  • 1Life and Health Sciences Laboratory, FMPT, Abdelmalek Essaadi University, Tetouan, Morocco.

Bioinformatics and Biology Insights
|January 28, 2026
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Summary
This summary is machine-generated.

SeqExpressionAnalyser is a new R package that simplifies differential gene expression analysis of RNA Sequencing (RNA-Seq) data. This user-friendly tool integrates the entire workflow, making complex analyses accessible to R users.

Keywords:
RRNA-Seqdifferential expressioninteractive data analysisweb application

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Differential gene expression analysis of RNA Sequencing (RNA-Seq) data is vital for understanding biological processes and diseases.
  • Current workflows involve manually combining multiple tools and scripts, which is time-consuming and not user-friendly, especially for non-experts.

Purpose of the Study:

  • To develop an integrated, automated, and accessible solution for RNA-Seq differential gene expression analysis.
  • To provide a user-friendly platform that unifies the entire analysis process for R users.

Main Methods:

  • Developed SeqExpressionAnalyser, an R package with a web application built on the Shiny framework.
  • The package enables users to perform quality control, filtering, alignment, read counting, and differential expression analysis on FASTQ files.

Main Results:

  • SeqExpressionAnalyser offers an interactive and unified platform for RNA-Seq data analysis.
  • The tool generates comprehensive outputs including data tables, HTML reports, and visualizations.
  • Source code is available on GitHub under GPLv3 license, and a Docker image is provided.

Conclusions:

  • SeqExpressionAnalyser addresses the need for an accessible and automated solution for RNA-Seq differential gene expression analysis.
  • The package empowers R users, including non-experts, to conduct complex analyses efficiently.