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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

Experts in RNA-seq analysis

They share and annotate bioinformatics tools

  • Rekin's Janky's avatar image
    Rekin's Janky
    Laboratory of Computational Biology, KU Leuven Center for Human Genetics, Leuven, Belgium
  • Bogdan Mirauta's avatar image
    Bogdan Mirauta
    Laboratory of Computational and Quantitative Biology, University Pierre et Marie Curie, Paris, France
  • Mikhail Shugay's avatar image
    Mikhail Shugay
    Genomics of Adaptive Immunity Lab, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science (RAS), Moscow, Russia
  • Abdoulaye Baniré Diallo's avatar image
    Abdoulaye Baniré Diallo
    Department of Computer Sciences, University of Quebec in Montreal, Montreal, Canada
  • Antoine Rousselin's avatar image Antoine Rousselin's country flag
    Antoine Rousselin
    Centre François Baclesse

Most recent bioinformatics tools

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MAQGene
Desktop

MAQGene

Allows read alignment as well as single nucleotide polymorphism (SNP) detection…

Allows read alignment as well as single nucleotide polymorphism (SNP) detection and annotation. MAQGene launches the MAQ software and assembles a customized summary of the location and specific…

LitPathExplorer
Web

LitPathExplorer

Allows exploration of literature-enriched pathway models. LitPathExplorer is a…

Allows exploration of literature-enriched pathway models. LitPathExplorer is a visual analytics tool that combines visual interactive analysis with state-of-heart text mining and semi-supervised…

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kCombine
Desktop

kCombine

Builds large assemblies thanks to the utilization of memory-intensive de novo…

Builds large assemblies thanks to the utilization of memory-intensive de novo transcriptome assembly algorithms. kCombine is a divide-and-conquer strategy that was tested on Schizosaccharomyces…

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BOAT
Desktop

BOAT Bayesian Overlap Analysis Tool

Identifies variants associated with two traits and tests for enrichment. BOAT…

Identifies variants associated with two traits and tests for enrichment. BOAT can be used to identify overlap variants between two traits by comparing Approximate Bayes Factor (ABF), as well as by…

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…

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