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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

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OMIC_12665
RNA editing

RES-Scanner

A flexible and efficient software package that detects and annotates RNA-editing sites…

A flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples. To rigorously identify potential false positives resulting from genetic variants, we…

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OMIC_12659
Gene set analysis

DEsubs

A flexible, computationally fast and efficient tool for exploring disease-associated gene…

A flexible, computationally fast and efficient tool for exploring disease-associated gene perturbations contextualized by subpathways in a graph-theoretic framework. DEsubs contains an extensive and customized framework with a broad range of…

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OMIC_12654
Normalization/differential…

Local-Pooled-Error with RNA-sequencing data
LPEseq

A method for differential expression (DE) analysis with a small number of replicates,…

A method for differential expression (DE) analysis with a small number of replicates, especially when a single replicate in each class is available. By extending the LPE method, the proposed method is applicable to the RNA-Seq experiments either…

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OMIC_12631
Normalization/differential…

Differential Expression Analysis based on RNA-seq data – Online
DEAR-O

A user-friendly platform for performance evaluation of differential expression analysis…

A user-friendly platform for performance evaluation of differential expression analysis based on RNA-seq data. DEAR-O currently includes four of the most popular tools: DESeq, DESeq2, edgeR and Cuffdiff2. Based on the DEAR-O platform, researchers…

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.

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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…

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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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