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Intron retention identification software tools | RNA sequencing data analysis

Alternative splicing (AS) affects up to 95% of multi-exonic genes in humans (Pan et al., 2008). The three main types of AS are exon skipping, alternative 5′ or 3′ usage and intron retention (IR). IR occurs when an intron is transcribed…
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MISO
Desktop

MISO

A probabilistic framework that quantitates the expression level of…

A probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.

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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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KMA
Desktop

KMA KeepMeAround

Analyzes intron retention (IR) in RNA-seq data. KMA was used to study IR in…

Analyzes intron retention (IR) in RNA-seq data. KMA was used to study IR in populations of human erythroblasts from proE to orthoE. It performs intron retention estimation and detection using…

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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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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…

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IRFinder
Desktop

IRFinder

Identifies correctly intron retention (IR) events and measured the ratio of…

Identifies correctly intron retention (IR) events and measured the ratio of retained introns to correctly spliced introns with great accuracy. IRFinder was developed to accurately detect IR from mRNA…

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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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iREAD
Desktop

iREAD intron REtention Analysis and Detector

Serves for the detection of genome-wide. iREAD works with both single-end and…

Serves for the detection of genome-wide. iREAD works with both single-end and paired-end sequencing data that has been prepared using poly-A enrichment. The resulting intron retention contents can be…

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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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IRclassifier
Desktop

IRclassifier Intron Retention classifier

A supervised machine learning-based approach for IR event detection from…

A supervised machine learning-based approach for IR event detection from RNA-Seq data. IRclassifier chooses J48 Decision Tree and Random Forest as the classification algorithms. IRclassifier is…

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IntEREst
Desktop

IntEREst Intron Exon Retention Estimator

Performs intron-exon retention analysis on RNA-seq data. IntEREst facilitates…

Performs intron-exon retention analysis on RNA-seq data. IntEREst facilitates estimation and comparison of splicing efficiency of various transcripts across several samples. It can estimate the…

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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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ASpli
Desktop

ASpli

Simplifies the characterization of genome-wide changes in alternative splicing…

Simplifies the characterization of genome-wide changes in alternative splicing (AS) under different experimental conditions. ASpli analyzes the differential usage of introns, exons, and splice…

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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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Erythroid…
Desktop

Erythroid Intron Retention Analysis

Allows to make intron retention analysis for erythroid development and…

Allows to make intron retention analysis for erythroid development and erythroid differentiation.

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IRcall
Desktop

IRcall Intron Retention call

A computational tool for intron retention (IR) event detection from RNA-Seq…

A computational tool for intron retention (IR) event detection from RNA-Seq data. IRcall calculates the IRscore, which combines information on three aspects: (a) ratio of RPKM within an intron to…

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