RNA sequencing data analysis bioinformatics software tools

RNA sequencing (RNA-seq) also known as whole transcriptome shotgun sequencing (WTSS) is the next-generation sequencing technology to study the transcriptome. It could be used as an alternative to microarrays for gene expression analysis, without the need to know the RNA sequence…

RNA-seq analysis steps

Data preprocessing

Data processing

Data analysis

Annotation

Interpretation

Data visualization

Pipelines & Utilities

RNA-seq analysis workflow

Click the icons of the schema to view tools

RNA-seq analysis workflow schema

Most recent bioinformatics tools

MG Workbench
Dataset

MG Workbench Microbial Genome Workbench

Explores bacterial and archaeal genomes. MG Workbench is a database designed to…

Explores bacterial and archaeal genomes. MG Workbench is a database designed to focus on intra-genomic and inter-genomic comparison of genes and proteins.

ePlant
Web

ePlant

Allows exploration of Arabidopsis thaliana through multiple levels. ePlant…

Allows exploration of Arabidopsis thaliana through multiple levels. ePlant permits researchers to extract information from their data. It can identify connections between layers and facilitate…

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Arabidopsis…
Web

Arabidopsis eFP Browser

Allows exploration of Arabidopsis microarray data to permit intuitive…

Allows exploration of Arabidopsis microarray data to permit intuitive visualization of gene expression data across approximately 22,000 genes from Arabidopsis thaliana. Arabidopsis eFP Browser allows…

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Expression…
Web

Expression Angler

Identifies genes showing similar expression or response profiles from selected…

Identifies genes showing similar expression or response profiles from selected databases. Expression Angler employs the Pearson correlation coefficient to identify co-regulated genes. It provides…

Most popular analytical software

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VENNY
Web

VENNY

Allows comparison of lists with Venn Diagrams. VENNY is a web-server,…

Allows comparison of lists with Venn Diagrams. VENNY is a web-server, consisting in a single standard html file that can be used off-line.

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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

ZENBU
Web

ZENBU

Enables data exploration through "on-demand" data processing and…

Enables data exploration through "on-demand" data processing and interactive linked-visualizationsthus enabling concurrent views from the same mere primary sequence alignment data which…

Curators for RNA-seq analysis

  • Rekin's Janky's avatar image
    Rekin's Janky
    Laboratory of Computational…
  • Bogdan Mirauta's avatar image
    Bogdan Mirauta
    Laboratory of Computational and…
  • Mikhail Shugay's avatar image
    Mikhail Shugay
    Genomics of Adaptive Immunity Lab,…
  • Abdoulaye Baniré Diallo's avatar image
    Abdoulaye Baniré Diallo
    Department of Computer Sciences,…
  • Antoine Rousselin's avatar image Antoine Rousselin's country flag
    Antoine Rousselin
    Centre François Baclesse

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