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Allele-specific expression detection software tools | RNA sequencing data analysis

RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants.Source text:(Pirinene et al.,…
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RNA2DNAlign
Desktop

RNA2DNAlign

Evaluates evidence of allelic imbalance and asymmetry of DNA and RNA sequencing…

Evaluates evidence of allelic imbalance and asymmetry of DNA and RNA sequencing datasets. RNA2DNAlign identifies allelic distributions corresponding to the following events: RNA editing (RNAed),…

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MBASED
Desktop
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IDP-ASE
Desktop

IDP-ASE

Allows users to quantify Allele-specific expression (ASE) at both the gene and…

Allows users to quantify Allele-specific expression (ASE) at both the gene and gene isoform levels. IDP-ASE integrates third generation-sequencing (TGS) and second-generation sequencing (SGS) data…

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QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

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ALEA
Desktop

ALEA

A computational toolbox for allele-specific epigenomics analysis, which…

A computational toolbox for allele-specific epigenomics analysis, which incorporates allelic variation data within existing resources, allowing for the identification of significant associations…

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Allelome.PRO
Desktop

Allelome.PRO Allelome Profiler

A user-friendly pipeline to investigate allele specific features in…

A user-friendly pipeline to investigate allele specific features in high-throughput data using any compatible annotation and SNP file. Allelome.PRO extends approaches used in previous studies that…

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ASARP
Desktop

ASARP Allele-Specific Alternative mRNA Processing

A method to identify genetically influenced mRNA processing events using…

A method to identify genetically influenced mRNA processing events using transcriptome sequencing (RNA-Seq) data. The method examines RNA-Seq data at both single-nucleotide and whole-gene/isoform…

MAMBA
Desktop

MAMBA

A computer program for the analysis and interpretation of genomics data with an…

A computer program for the analysis and interpretation of genomics data with an emphasis on understanding the genetic basis of biomedical traits. In MAMBA, statistical methods for the analysis of…

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QuASAR
Desktop

QuASAR Quantitative Allele Specific Analysis of Reads

Jointly detects heterozygous genotypes and infers allele-specific expression…

Jointly detects heterozygous genotypes and infers allele-specific expression (ASE). QuASAR is a statistical learning method that starts from a single or multiple RNA-seq experiments from the same…

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ASEQ
Desktop

ASEQ

A tool to perform gene-level allele-specific expression (ASE) analysis from…

A tool to perform gene-level allele-specific expression (ASE) analysis from paired genomic and transcriptomic NGS data without requiring paternal and maternal genome data. ASEQ offers an easy-to-use…

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AllelicImbalanc…
Desktop

AllelicImbalance

Detects, manages and visualizes allelic imbalances. AllelicImbalance allows…

Detects, manages and visualizes allelic imbalances. AllelicImbalance allows users to ask genetic questions in any RNA sequencing experiment. It contains a visualization mode assisting users in notice…

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ASE-TIGAR
Desktop

ASE-TIGAR

A Bayesian approach to estimate allele-specific expression (ASE) from RNA…

A Bayesian approach to estimate allele-specific expression (ASE) from RNA sequencing data with diploid genome sequences. In the statistical framework, the haploid choice is modeled as a hidden…

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SCALE
Desktop

SCALE Single Cell ALlelic Expression

Analyzes genome-wide allele-specific bursting. SCALE permits adjustment of…

Analyzes genome-wide allele-specific bursting. SCALE permits adjustment of technical variability. It detects genes exhibiting allelic differences in bursting parameters, and genes whose alleles burst…

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EMASE
Desktop

EMASE Expectation-Maximization algorithm for Allele Specific Expression

Simultaneously quantifies allele-specific expression and gene expression from…

Simultaneously quantifies allele-specific expression and gene expression from RNA-seq data. EMASE is the implementation of an expectation maximization (EM) algorithm that accounts for the…

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AlleleSeq
Desktop

AlleleSeq

With the evolution of DNA sequencing technology, it is now possible to study…

With the evolution of DNA sequencing technology, it is now possible to study expression and DNA binding differences between pairs of sequence alleles on the maternally- and paternally-derived…

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iASeq
Desktop

iASeq

Uses a Bayesian hierarchical mixture model to learn correlation patterns of…

Uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. Using the discovered correlation patterns, the model allows one to borrow…

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A flexible…
Algorithm

A flexible Bayesian model for analysis of allelic imbalance

A flexible Bayesian model for analysis of allelic imbalance (AI), which…

A flexible Bayesian model for analysis of allelic imbalance (AI), which accounts for bias and can be implemented without DNA controls. In lieu of DNA controls, this Poisson-Gamma (PG) model uses an…

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Allele…
Desktop

Allele workbench

Reduces allele bias by creating a variant masked genome. Allele workbench…

Reduces allele bias by creating a variant masked genome. Allele workbench provides both heterozygous single nucleotide polymorphisms (SNP) coverage and isoform-aware read counts. It utilizes the…

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Allim
Desktop

Allim ALLelic Imbalance Metre

Allows users to measure allele specific gene expression (ASE). Allim is a…

Allows users to measure allele specific gene expression (ASE). Allim is a standalone software composed of five modules to (i) Determine fixed single nucleotide polymorphism (SNPs) and create two…

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cisASE
Desktop

cisASE

A likelihood-based method for detecting allele-specific expression (ASE) on…

A likelihood-based method for detecting allele-specific expression (ASE) on single nucleotide variant (SNV), exon and gene levels from sequencing data without requiring phasing or parental…

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