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Alternative splicing identification software tools | Gene expression microarray data analysis

The analysis of differential splicing (DS) is crucial for understanding physiological processes in cells and organs. In particular, aberrant transcripts are known to be involved in various diseases including cancer. A widely used technique for…
PLATA
Desktop
G T A T C G C T A
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…

IGEMS
Desktop

IGEMS Integrated Gene and Exon Model of Splicing

A robust methodology for detection of alternative exon usage (AEU) events using…

A robust methodology for detection of alternative exon usage (AEU) events using global transcriptome data, yielding results with limited requirement for visual inspection and a high true positive…

PECA
Desktop

PECA Probe-level Expression Change Averaging

Recognizes differential expression in Affymetrix gene expression microarray…

Recognizes differential expression in Affymetrix gene expression microarray studies. PECA calculates the probe-level expression changes using the ordinary or modified t-statistic. This tool can also…

EventPointer
Desktop

EventPointer

Searches and analyzes alternative splicing (AS) events using Human…

Searches and analyzes alternative splicing (AS) events using Human Transcriptome Array 2.0 (HTA 2.0). EventPointer uses a linear model that broadens its application from plain case-control studies to…

MEAP
Desktop

MEAP Multiple Exon Array Preprocessing

An R package that is designed to preprocess, analyze and visualize Affymetrix…

An R package that is designed to preprocess, analyze and visualize Affymetrix GeneChip exon array data. MEAP contains modules for data pre-processing, differential expression analysis, and…

SpliceMiner
Web

SpliceMiner

Allows to query Evidence Viewer Database (EVDB). SpliceMiner maps probes to…

Allows to query Evidence Viewer Database (EVDB). SpliceMiner maps probes to splice variants. The database contains non-redundant compendium of splice variant data for human genes. It can be searched…

puma
Desktop

puma

Provides methods for gene and transcript expression summarisation and…

Provides methods for gene and transcript expression summarisation and uncertainty propagation methods for the downstream analysis. puma supports a wide range of quantitative expression analysis of…

COSIE
Desktop

COSIE Corrected Splicing Indices for Exon Arrays

An R function that for a given set of exon arrays corrects for the observed…

An R function that for a given set of exon arrays corrects for the observed bias and improves the detection of alternative splicing. COSIE adjusts splicing indices for exons, especially for those…

MMBGX
Desktop

MMBGX Multi-Mapping Bayesian Gene eXpression

Disaggregates the signal at 'multi-match' probes. When applied to…

Disaggregates the signal at 'multi-match' probes. When applied to Gene arrays, MMBGX removes the upward bias of gene-level expression estimates. When applied to Exon arrays, it can further…

MADS+
Desktop

MADS+

A computational pipeline to detect differential splicing events from the…

A computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting…

ANOSVA
Desktop

ANOSVA ANalysis Of Splice VAriation

A statistical method to detect alternative splicing from expression data. Since…

A statistical method to detect alternative splicing from expression data. Since ANOSVA requires no transcript information, it can be applied when the level of annotation is poor. When validated…

ARH
Desktop

ARH

An entropy-based measure for splicing prediction. ARH is based on a simple,…

An entropy-based measure for splicing prediction. ARH is based on a simple, robust model based on the exon expression ratios with respect to two experimental conditions. A deviation in exons leads to…

FIRMA
Desktop

FIRMA Finding Isoforms using Robust Multichip Analysis

A method for detecting differential alternative splicing in exon array data.…

A method for detecting differential alternative splicing in exon array data. FIRMA has been developed for Affymetrix exon arrays, but could in principle other exon arrays, tiling arrays or splice…

MADS
Desktop

MADS Microarray Analysis of Differential Splicing

A method for discovery of differential alternative splicing from exon-tiling…

A method for discovery of differential alternative splicing from exon-tiling microarray data. MADS incorporates a series of low-level analysis algorithms motivated by the "probe-rich"…

TIPMaP
Web

TIPMaP Transcript Isoform Profiles from Microarray Probes

A web server for expression profiling of alternatively spliced transcripts…

A web server for expression profiling of alternatively spliced transcripts using microarray data sets from 31 standard 3' Affymetrix arrays for human, mouse and rat species. TIPMaP has been…

easyExon
Desktop

easyExon

A Java-based freeware to process, filtrate and visualize exon array data with…

A Java-based freeware to process, filtrate and visualize exon array data with an analysis pipeline. This tool implements the most commonly used probeset summarization methods as well as AS-orientated…

ExonMiner
Web

ExonMiner

A web service for analysis of exon array data to detect transcripts that have…

A web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following…

REMAS
Algorithm

REMAS

An improved regression model to select alternatively spliced genes and exons…

An improved regression model to select alternatively spliced genes and exons from exon array data. Both simulation and real data analysis indicate that REMAS has convincing capability in…

MIDAS
Desktop

MIDAS Microarray Data Analysis System

A Java application, provides users an intuitive interface to design analysis…

A Java application, provides users an intuitive interface to design analysis protocols combining one or more normalization and filtering steps. MIDAS provides scatterplots that illustrate the effects…

G T A T C G C T A
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,…

Rmodel
Desktop

Rmodel

Provides a probe-level analysis of gene expression microarray data. Rmodel is…

Provides a probe-level analysis of gene expression microarray data. Rmodel is an open-source package which allows users to segment a microarray probe set to identify novel processing events. The…

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