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Differential usage software tools | RNA sequencing data analysis

It is important to distinguish differential transcript usage (DTU) from gene-level differential expression and from transcript-level differential expression (DTE). In particular, DTU considers changes in the proportions of the isoforms of a gene…
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Cuffdiff
Desktop

Cuffdiff

An algorithm that estimates expression at transcript-level resolution and…

An algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries.

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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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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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rMATS
Desktop

rMATS replicate Multivariate Analysis of Transcript Splicing

A statistical model and computer program designed for detection of differential…

A statistical model and computer program designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for…

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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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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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IsoEM/IsoDE
Desktop

IsoEM/IsoDE

Allows expression level estimation and differential expression (DE) from…

Allows expression level estimation and differential expression (DE) from RNA-Seq data. IsoEM uses bootstrapping to infer confidence intervals for gene and isoform expression level estimates. The…

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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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Solas
Desktop

Solas

A package for the statistical language R, devoted to the analysis of next…

A package for the statistical language R, devoted to the analysis of next generation short read data of transcripts, generally called RNA-Seq.

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GPSeq
Desktop

GPSeq

This is a software tool to analyze RNA-seq data to estimate gene and exon…

This is a software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons. The usefulness of the GP model is…

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FineSplice
Desktop

FineSplice

A pipeline based on TopHat2 combined with a splice junction detection algorithm.

A pipeline based on TopHat2 combined with a splice junction detection algorithm.

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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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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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stageR
Desktop

stageR

Allows user-friendly automated stage-wise analysis of high-throughput genomic…

Allows user-friendly automated stage-wise analysis of high-throughput genomic data. stageR implements two-stage testing as a general paradigm for assessing high throughput experiments involving…

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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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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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JETTA
Desktop

JETTA

It was developed to detect alternatively spliced exons between two conditions,…

It was developed to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study.

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iso-kTSP
Desktop

iso-kTSP

A computational method, robust to biological and technical variability, which…

A computational method, robust to biological and technical variability, which identifies significant transcript isoform changes across multiple samples. iso-kTSP reveals novel signatures of cancer in…

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DRIMSeq
Desktop

DRIMSeq

Performs gene-level tests and returns p-values per gene only. DRIMSeq provides…

Performs gene-level tests and returns p-values per gene only. DRIMSeq provides two frameworks. One for the differential splicing analysis between different conditions and one for the sQTL analysis.…

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jSplice
Desktop

jSplice

A junction-centric method that enables de novo extraction of alternative…

A junction-centric method that enables de novo extraction of alternative splicing events from RNA-sequencing data with high accuracy, reliability, and speed. Unlike Spanki and rMATS, which rely on…

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ARH-seq
Desktop

ARH-seq

A discovery tool for differential splicing in case-control studies that is…

A discovery tool for differential splicing in case-control studies that is based on the information-theoretic concept of entropy.

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BayCount
Desktop

BayCount

Infers tumor transcriptional heterogeneity using RNA-Seq count data. BayCount…

Infers tumor transcriptional heterogeneity using RNA-Seq count data. BayCount is a Bayesian matrix decomposition model that takes into account both random effects between samples and specific genetic…

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BayesDRIMSeq
Desktop

BayesDRIMSeq

Infers genes with differential transcript usage. BayesDRIMSeq is a count-based…

Infers genes with differential transcript usage. BayesDRIMSeq is a count-based method proceeding to a transformation of the whole sequence of posterior probabilities with respect to the ordering of…

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cjBitSeq
Desktop

cjBitSeq

Quantifies the transcriptome of a given organism or cell. cjBitSeq allows…

Quantifies the transcriptome of a given organism or cell. cjBitSeq allows production of transcriptomic data and can be used to reconstruct the transcriptome using de novo or guided assembly, or to…

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RATs
Desktop

RATs Relative Abundance of Transcripts

Supplies a way to detect changes in the abundance ratios of transcript isoforms…

Supplies a way to detect changes in the abundance ratios of transcript isoforms of a gene, this method is named Differential Transcript Usage (DTU). The RATs method serves for identification and…

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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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SwitchSeq
Desktop

SwitchSeq

A tool to identify, annotate and visualise splicing switch events from RNA-seq…

A tool to identify, annotate and visualise splicing switch events from RNA-seq data. By relying on transcript level quantifications, SwitchSeq provides a simple (yet powerful) approach to identify,…

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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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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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SEVA
Algorithm

SEVA Splice Expression Variation Analysis

An algorithm to simultaneously account for tumor heterogeneity and mitigate…

An algorithm to simultaneously account for tumor heterogeneity and mitigate confounding of alternative splicing events (ASEs) with differentially expressed genes. SEVA compares the degree of…

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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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IUTA
Desktop

IUTA Isoform Usage Two-step Analysis

An analysis tool of Illumina paired-end mRNA-seq data for detecting…

An analysis tool of Illumina paired-end mRNA-seq data for detecting differential usage of gene transcript isoforms. It first uses the EM algorithm to identify the usage of transcript isoforms for…

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RACKJ
Desktop

RACKJ Read Analysis & Comparison Kit in Java

A set of Java programs that analyze and compare RNA-seq data made by NGS…

A set of Java programs that analyze and compare RNA-seq data made by NGS technologies. In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing…

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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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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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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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IsoformSwitchAn…
Desktop

IsoformSwitchAnalyzeR

Identifies and analysis the potential consequences of isoform switches from…

Identifies and analysis the potential consequences of isoform switches from RNA-seq derived quantification of both novel and annotated full-length isoforms. IsoformSwitchAnalyzeR is an easy to use R…

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Quantas
Desktop

Quantas

A pipeline to analyze alternative splicing using RNA-Seq. gapless and countit…

A pipeline to analyze alternative splicing using RNA-Seq. gapless and countit are collectively named Quantas. The pipeline has been tested quite extensively, but the document is still at its…

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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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FDM
Desktop

FDM flow difference metric

Detects differential transcription between pairs of samples or between groups…

Detects differential transcription between pairs of samples or between groups of replicates. FDM is based on a statistical method for performing a permutation test on ACT-Graphs that does not depend…

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