RNA sequencing data analysis bioinformatics software tools

RNA-seq analysis steps

Preprocessing & quality control

Data analysis

Annotation & interpretation

File, data & workflows

RNA-seq analysis workflow

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RNA-seq analysis workflow schema
In recent years, the continuing technical improvements and decreasing cost of next-generation sequencing technology have made RNA sequencing (RNA-seq) a popular choice for gene expression studies (Wang et al., 2009; Ozsolak and Milos, 2011). Such…

RNA sequencing data analysis bioinformatics software tools

Most Recent Tools

Desktop app
G T A T C G C T A svaseq svaseq

svaseq

Uses surrogate variable analysis (sva) for estimating unwanted noise and…

Uses surrogate variable analysis (sva) for estimating unwanted noise and unmodeled artifacts by (i) identifying the part of the genomic data only affected by artifacts and (ii) estimating the…

Desktop app
G T A T C G C T A viGEN viGEN

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and…

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first…

Desktop app
Pse-Analysis Pse-Analysis

Pse-Analysis

Expedites the pace in conducting genome/proteome analysis. Pse-Analysis can…

Expedites the pace in conducting genome/proteome analysis. Pse-Analysis can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3)…

Web app
Desktop app
G T A T C G C T A Differential Gene… Differential Gene Expression Interactive Visual…

DEIVA Differential Gene Expression Interactive Visual Analysis

Enables locating and identifying single or multiple genes in an immediate,…

Enables locating and identifying single or multiple genes in an immediate, interactive, and intuitive manner. DEIVA offers a unique combination of design decisions that enable inspection and analysis…

Most Popular Tools

Desktop app
G T A T C G C T A RNA-eXpress RNA-eXpress

RNA-eXpress

It was designed as a user friendly solution to extract and annotate…

It was designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data.

Desktop app
G T A T C G C T A RNA-Seq by… RNA-Seq by Expectation-Maximization

RSEM RNA-Seq by Expectation-Maximization

An user-friendly software package for quantifying gene and isoform abundances…

An user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data.

Desktop app
G T A T C G C T A EBARDenovo EBARDenovo

EBARDenovo

Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.

Desktop app
Blast2GO Blast2GO

Blast2GO

A comprehensive bioinformatics tool for functional annotation of sequences and…

A comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes…

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 BanirĂ© Diallo's avatar image
    Abdoulaye Baniré Diallo
    Department of Computer Sciences,…

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