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Alternative splicing event visualization software tools | RNA sequencing data analysis

Alternative splicing is involved in many biological phenomena and has been better evidenced due to the development of next-generation sequencing (NGS) technologies (Trapnell et al., 2009). RNA-Seq technologies have facilitated the deep…
IGV
Desktop

IGV Integrative Genomics Viewer

A high-performance viewer that efficiently handles large heterogeneous data…

A high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of…

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EASANA
Web

EASANA

Allows to display microarray data in their genomic context. EASAN is a…

Allows to display microarray data in their genomic context. EASAN is a user-friendly interface to genome-wide gene expression studies using microarrays and Next Generation Sequencing (NGS). This tool…

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ALEXA-Seq
Desktop

ALEXA-Seq

A method for using massively parallel paired-end transcriptome sequencing for…

A method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.

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DEXSeq
Desktop

DEXSeq

Tests for differential usage of exons and hence of isoforms in RNA-seq samples.…

Tests for differential usage of exons and hence of isoforms in RNA-seq samples. DEXSeq uses generalized linear models and offers reliable control of false discoveries by taking biological variation…

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JunctionSeq
Desktop

JunctionSeq

An R/Bioconductor package that builds on the statistical techniques used by the…

An R/Bioconductor package that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In…

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SpliceGrapher
Desktop

SpliceGrapher

Predicts alternative splicing patterns and produces splice graphs that capture…

Predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene's exons may be assembled. SpliceGrapher enhances gene models using evidence…

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expressRNA
Web

expressRNA

Processes 3’ mRNA sequencing data. expressRNA classifies the sites where…

Processes 3’ mRNA sequencing data. expressRNA classifies the sites where cleavage and polyadenylation take place. It is able to identify the differentially regulated poly(A) sites. This tool…

Savant
Desktop

Savant

A next-generation genome browser designed for the latest generation of genome…

A next-generation genome browser designed for the latest generation of genome data.

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MAJIQ-SPEL
Web

MAJIQ-SPEL MAJIQ for Sampling Primers and Evaluating Local splicing variations

Helps in the visualization, interpretation, and experimental validation of both…

Helps in the visualization, interpretation, and experimental validation of both classical and complex splicing variations. MAJIQ-SPEL offers researchers fast and accurate primer design for de novo…

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Manananggal
Desktop

Manananggal

Uses to detect alternative splicing events (ASEs). This application written in…

Uses to detect alternative splicing events (ASEs). This application written in Java can, through a web application, scans RNAseq data to identify them, and Manananggal can also be launched as a…

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MAJIQ
Desktop

MAJIQ Modeling Alternative Junction Inclusion Quantification

Provides a method to detect, quantify and visualize differential splicing…

Provides a method to detect, quantify and visualize differential splicing between groups of experiments. Two key features distinguish MAJIQ from other algorithms. First, MAJIQ does not quantify whole…

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Snaptron
Web
Desktop

Snaptron

Allows users to search and summarize RNA sequencing data. Snaptron is a search…

Allows users to search and summarize RNA sequencing data. Snaptron is a search engine for querying splicing patterns in large, pre-analyzed collections about human. It lends valuable context and…

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AVISPA
Web

AVISPA Advanced Visualization of Splicing Prediction and Analysis

Splices prediction and analysis. AVISPA predicts whether the exon is…

Splices prediction and analysis. AVISPA predicts whether the exon is alternatively spliced, displays tissue-dependent splicing patterns, and whether it has associated regulatory elements. The tool…

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SplicingCompass
Desktop

SplicingCompass

A package to predict genes that are differentially spliced between two…

A package to predict genes that are differentially spliced between two different conditions using RNA-seq data. This method allows users to detect tissue-specific alternative splicing in brain versus…

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SpliceSeq
Desktop

SpliceSeq

A tool for investigating alternative mRNA splicing in next generation mRNA…

A tool for investigating alternative mRNA splicing in next generation mRNA sequence data. SpliceSeq displays intuitive visualizations and prioritized lists of results that highlight splicing events…

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SplicePlot
Desktop

SplicePlot

A package for visualizing alternative splicing and the effects of splicing…

A package for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. SplicePlot takes mapped RNA sequencing reads and genotype data as input…

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Cascade
Web

Cascade

A tool for the visualization of RNA-seq data from cancer genomics projects,…

A tool for the visualization of RNA-seq data from cancer genomics projects, which has the advantages of providing researchers with an intuitive interface for exploring their data in the context of…

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Vials
Desktop

Vials VIsualizing ALternative Splicing

Allows analysis of isoform data for large-scale RNA-seq experiments. Vials…

Allows analysis of isoform data for large-scale RNA-seq experiments. Vials permits identification of isoform distributions across individual samples or groups of samples and comparison between…

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Sashimi plots
Desktop

Sashimi plots

A quantitative visualization of aligned RNA-Seq reads that enables quantitative…

A quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. Sashimi plots can be made using the Broad…

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SplicingViewer
Desktop

SplicingViewer

Developed for unambiguous detection, annotation and visualization of splice…

Developed for unambiguous detection, annotation and visualization of splice junctions and alternative splicing events from RNA-Seq data.

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Splicing…
Desktop

Splicing Express

Provides a simple and effective way for the identification, annotation and…

Provides a simple and effective way for the identification, annotation and visualization of Alternative Splicing Events (ASEs). Splicing Express is a software suite that provides expression graphics…

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Psichomics
Desktop

Psichomics

An R package with a Shiny-based graphical interface for the integrated analysis…

An R package with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). Psichomics interactively performs survival, principal…

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ASATP
Web
Desktop

ASATP Alternative Splicing Analysis Tool Package

A toolkit to analyze alternative splicing events. ASATP could be used to detect…

A toolkit to analyze alternative splicing events. ASATP could be used to detect and visualize alternative splicing events, check open reading frame (ORF) changes, assess regulations of alternative…

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ViennaNGS
Desktop

ViennaNGS

An integrated collection of Perl modules focused on building efficient…

An integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. ViennaNGS comes with functionality for extracting and converting features from common NGS…

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dSpliceType
Desktop

dSpliceType

A generalized framework to systematically investigate the synergistic and…

A generalized framework to systematically investigate the synergistic and antagonistic effects of differential splicing and differential expression. dSpliceType detects and prioritizes a list of…

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Sircah
Desktop

Sircah

An application written in python that detects and visualizes alternative…

An application written in python that detects and visualizes alternative splicing events using spliced alignments. Sircah takes as input transcript models in the GFF3 format allowing the user the…

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RSEQtools
Desktop

RSEQtools

A suite of tools that use this format for the analysis of RNA-Seq experiments.

A suite of tools that use this format for the analysis of RNA-Seq experiments.

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WASP
Web

WASP Website for Alternative Splicing Prediction

Combines subgroups of features into a network, allows different tissues to…

Combines subgroups of features into a network, allows different tissues to share feature subgroups. WASP uses hidden variables within a network architecture to model non-linear relationships between…

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