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RNA sequencing analysis software tools

High-throughput sequencing software tools

RNA-seq analysis applications

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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 sequence-based methods have revolutionized studies of the transcriptome by enabling a wide range of novel applications, including detection of alternative splicing isoforms and transcript fusion detection. In addition, RNA-seq has become an attractive alternative to microarrays for the identification of differentially expressed genes between several conditions or tissues.
Curators: Abdoulaye Baniré Diallo, Rekin's Janky, Bogdan Mirauta and Mikhail Shugay

RNA-seq analysis Curators
Rekin's Janky avatar
Rekin's Janky
Bogdan Mirauta avatar
Bogdan Mirauta
Mikhail Shugay avatar
Mikhail Shugay
Abdoulaye Baniré Diallo avatar
Abdoulaye Baniré Diallo

Most Recent Tools

new
OMIC_12850
Other tools

V'DJer

A software for inference of B-cell receptor (BCR) repertoires using short-read RNA…

A software for inference of B-cell receptor (BCR) repertoires using short-read RNA sequencing data. V'DJer uses customized read extraction, assembly and V(D)J rearrangement detection and filtering to produce contigs representing the most…

new
OMIC_12843
Normalization/differential…

timeSeq

A package for detecting the differentially expressed (DE) genes in time course RNA-Seq…

A package for detecting the differentially expressed (DE) genes in time course RNA-Seq data. The negative binomial mixed-effect model (NBMM) method is applied to gene expression data on a gene-by-gene basis. A parallel computing option is…

new
OMIC_12840
Circular RNA detection

FUll CHaracterization of circular RNA using RNA Sequencing
FUCHS

A python pipeline to characterize circRNAs candidates. FUCHS provides the user with…

A python pipeline to characterize circRNAs candidates. FUCHS provides the user with directions for further steps to investigate the circRNA’s function and biogenesis. FUCHS is able to identify alternative exon usage within the same circle…

new
OMIC_12839
Normalization/differential…

RiboDiff

Detects the protein translational efficiency change from Ribo-Seq (ribosome footprinting)…

Detects the protein translational efficiency change from Ribo-Seq (ribosome footprinting) and RNA-Seq data. RiboDiff uses a generalized linear model to detect genes showing difference in translational profile taking mRNA abundance into account. It…

Most Popular Tools

popular
OMIC_01287
Transcript quantification

RNA-Seq by Expectation-Maximization
RSEM

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

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

popular
OMIC_01317
De novo transcriptome assembly

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.

popular
OMIC_01475
Transcriptome annotation

Blast2GO

A comprehensive bioinformatics tool for functional annotation of sequences and data…

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 function transfer from homologous sequences through an…

popular
OMIC_07694
Gene prediction

CodingQuarry

A highly accurate, self-training GHMM fungal gene predictor designed to work with…

A highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. RNA-seq data informs annotations both during gene-model training and in prediction. This approach capitalises on the high…

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