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Alternative splicing detection software tools | RNA sequencing data analysis

Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis.Source text:(Wang…
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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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AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

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NGS-Trex
Web

NGS-Trex NGS TRanscriptome profile EXplorer

Allows user to upload raw sequences and obtain an accurate characterization of…

Allows user to upload raw sequences and obtain an accurate characterization of the transcriptome profile. NGS-Trex can assess differential expression at both gene and transcript level. It compares…

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AStalavista
Desktop
Web

AStalavista

Allows to dynamically identify, extract and display complex alternative…

Allows to dynamically identify, extract and display complex alternative splicing (AS) events from annotated genes. AStalavista is an alternative splicing transcriptional landscape visualization tool…

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spliceR
Desktop

spliceR

Sorts alternative splicing (AS) and discovers coding potential. spliceR…

Sorts alternative splicing (AS) and discovers coding potential. spliceR simplifies downstream sequence analysis by allowing annotation of genomic coordinates of the differentially spliced elements.…

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EBChangePoint
Desktop

EBChangePoint Empirical Bayes Change-Point model

An empirical Bayes change-point model to identify alternative 3' splice…

An empirical Bayes change-point model to identify alternative 3' splice sites (SS) and 5' SS. Compared with previous methods, our approach has several unique merits. First of all, our model…

Nematode.net
Dataset

Nematode.net

Disseminates diverse bioinformatic data sets and provide analysis tools to the…

Disseminates diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner. Next-generation data has been added to the various…

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SUPPA
Desktop

SUPPA

Allows to analyze differential splicing. SUPPA measures differential splicing…

Allows to analyze differential splicing. SUPPA measures differential splicing between conditions by exploiting the variability between biological replicates to determine the uncertainty in the…

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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…

SPLICIFY
Desktop

SPLICIFY

Identifies differentially expressed splice variants on RNA and protein level.…

Identifies differentially expressed splice variants on RNA and protein level. SPLICIFY is able to identify condition-specific aberrant splicing events on protein level by performing comparative…

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SpliceTrap
Desktop

SpliceTrap

A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq…

A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing.

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TSIS
Desktop

TSIS Time-Series Isoform Switch

Detects and characterizes temporal and complex isoform switches. TSIS…

Detects and characterizes temporal and complex isoform switches. TSIS recognizes pairs of alternative splicing (AS) transcripts with one or more isoform switches and genes with multiple pairs of…

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TRAPLINE
Desktop

TRAPLINE Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides…

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect…

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Spanki
Desktop

Spanki Splicing analysis kit

A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

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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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ExonFinder
Desktop

ExonFinder

A pipeline for the identification of novel exons/alternatively spliced variants…

A pipeline for the identification of novel exons/alternatively spliced variants (ASVs). ExonFinder is a large-scale comparative analysis of the expressed sequence tag (EST) library from nine grass…

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SplicePie
Desktop

SplicePie

A classification of RNA-Seq reads based on three major stages of splicing:…

A classification of RNA-Seq reads based on three major stages of splicing: pre-, intermediate- and post-splicing. SplicePie offers a number of approaches and solutions to study splicing in more…

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ISVASE
Desktop

ISVASE identifying sequence variants associated with splicing events

Recognizes sequence variants associated with splicing events (SVASE) by using…

Recognizes sequence variants associated with splicing events (SVASE) by using RNA-seq data. ISVASE is able to identify SVASEs for both parts of splicing event (or junction) separately. It applies…

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PreTIS
Web

PreTIS Prediction of translation initiation sites

Redicts the initiation confidence of all reading–frame independent start…

Redicts the initiation confidence of all reading–frame independent start sites (AUG and all near-cognate codons) located in the 5’ UTR of human mRNA sequences. PreTIS gives access to various…

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CASH
Desktop

CASH Comprehensive alternative splicing Hunting

Aims to self-construct alternative splicing (AS) sites and detect differential…

Aims to self-construct alternative splicing (AS) sites and detect differential AS events between samples of RNA-Seq data. CASH (Comprehensive alternative splicing hunting) consists of two major…

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IsoSeq_AS_de_no…
Desktop

IsoSeq_AS_de_novo

Characterizes and identifies bona fide alternatively spliced transcripts in any…

Characterizes and identifies bona fide alternatively spliced transcripts in any non-model system that lacks a reference genome sequence. IsoSeq_AS_de_novo can be applied to a non-model system with…

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SNPlice
Desktop

SNPlice

A computational approach for identifying cis-acting, splice-modulating variants…

A computational approach for identifying cis-acting, splice-modulating variants from RNA-seq datasets. SNPlice mines RNA-seq datasets to find reads that span single nucleotide variant (SNV) loci and…

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PSGInfer
Desktop

PSGInfer

Inference of alternative splicing from RNA-Seq data with probabilistic splice…

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

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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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ASprofile
Desktop

ASprofile

A suite of programs for extracting, quantifying and comparing alternative…

A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

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findAS
Desktop

findAS

A software tool for the analysis of alternatively spliced junctions. FindAS…

A software tool for the analysis of alternatively spliced junctions. FindAS requires RNA-seq data aligned against a reference genome and gene coordinates. Aligned reads are grouped together and…

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RAP
Web

RAP RNA-seq Analysis Pipeline

Allows users to analyze sequencing data in multiple steps. The RAP purpose is…

Allows users to analyze sequencing data in multiple steps. The RAP purpose is to investigate the complex transcriptional landscape of eukaryotic transcriptomes through a computationally optimized…

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nagnag
Desktop

nagnag

Predicts and quantifies the NAGNAG alternative splicing events using the…

Predicts and quantifies the NAGNAG alternative splicing events using the RNA-Seq data. nagnag fills a gap in the development of the tools for the accurate estimation of NAGNAG splicing events and…

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LeafCutter
Desktop

LeafCutter

Allows identification and quantification of novel and existing alternative…

Allows identification and quantification of novel and existing alternative splicing events by focusing on intron excisions. LeafCutter identifies variable intron splicing events from short-read…

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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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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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SplicingTypesAn…
Desktop

SplicingTypesAnno

Allows users to extract, annotate and analyze alternative splicing (AS) types…

Allows users to extract, annotate and analyze alternative splicing (AS) types for sequence alignment files from RNA-Seq. SplicingTypesAnno can detect the novel splicing directly from the aligned raw…

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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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ASFinder
Desktop

ASFinder Alternatively Splicing Finder

Discovers Alternatively Splicing (AS) transcripts from Expressed Sequence Tag…

Discovers Alternatively Splicing (AS) transcripts from Expressed Sequence Tag (EST)-derived sequences. ASFinder was able to identify AS isoforms using Aspergills niger EST-derived sequences and…

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ChopStitch
Desktop

ChopStitch

Retrieves putative exons and builds splice graphs. ChopStitch employs an…

Retrieves putative exons and builds splice graphs. ChopStitch employs an assembled transcriptome and whole genome shotgun sequencing (WGSS) data to proceed. Using a Bloom filter, it can recognize…

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PAVFinder
Desktop

PAVFinder Post Assembly VariantFinder

Identifies structural variants from de novo assemblies. PAVFinder is able to…

Identifies structural variants from de novo assemblies. PAVFinder is able to detect translocations, inversions, duplications, insertions, deletions, simple-repeat expansions/contractions for genomic…

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outrigger
Desktop

outrigger

Uses junction reads from RNA seq data, and a graph database to create a de novo…

Uses junction reads from RNA seq data, and a graph database to create a de novo alternative splicing annotation with a graph database. Outrigger is a Python package and an RNA-seq analysis software…

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SpliCQ
Desktop

SpliCQ

A Java software package which allows for the identification of splicing events…

A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.

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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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Array Studio
Desktop

Array Studio

Provides the premier enterprise solution for data content, framework and…

Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…

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RASA
Desktop

RASA Robust Alternative Splicing Analysis

Analyzes alternative splicing (AS) of human transcriptome arrays (HTA)…

Analyzes alternative splicing (AS) of human transcriptome arrays (HTA) platforms and similar exon-junction arrays to reduce the false positives. RASA calculates the expression index of each gene,…

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