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Known isoform quantification software tools | RNA-seq analysis

Transcript identification and the quantification of gene expression have been distinct core activities in molecular biology ever since the discovery of RNA’s role as the key intermediate between the genome and the proteome. Scientists plan…
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Cufflinks
Desktop

Cufflinks

Assembles transcripts, estimates their abundances, and tests for differential…

Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

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BitSeq
Desktop

BitSeq Bayesian inference of transcripts from sequencing data

An application for inferring expression levels of individual transcripts from…

An application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach…

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RSEM
Desktop

RSEM RNA-Seq by Expectation-Maximization

An user-friendly software package for quantifying gene and isoform abundances…

An user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data.

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The FLUX…
Desktop

The FLUX CAPACITOR

The input for the FLUX CAPACITOR is the annotation of a reference transcriptome…

The input for the FLUX CAPACITOR is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome.

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RNA-eXpress
Desktop

RNA-eXpress

It was designed as a user friendly solution to extract and annotate…

It was designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data.

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ReCount
Dataset

ReCount

Summarizes analysis-ready expression data for genes, exons, exon–exon splice…

Summarizes analysis-ready expression data for genes, exons, exon–exon splice junctions and base-level coverage. ReCount is an online resource that uses analysis pipelines that are annotation…

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alpine
Desktop

alpine

An R/Bioconductor package for modeling and correcting fragment sequence bias…

An R/Bioconductor package for modeling and correcting fragment sequence bias for RNA-seq transcript abundance estimation. This framework enables further research both into optimization of library…

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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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eXpress
Desktop

eXpress

A streaming tool for quantifying the abundances of a set of target sequences…

A streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.

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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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SeqMonk
Desktop

SeqMonk

A program to enable the visualisation and analysis of mapped sequence data.…

A program to enable the visualisation and analysis of mapped sequence data. SeqMonk was written for use with mapped next generation sequence data but can in theory be used for any dataset which can…

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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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rQuant
Desktop
Web

rQuant

Infers the abundance of given transcripts from RNA-Seq data. rQuant is a method…

Infers the abundance of given transcripts from RNA-Seq data. rQuant is a method based on solving quadratic programming problems. The software achieves the highest accuracy when estimating density…

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rnaseqcomp
Desktop

rnaseqcomp

Evaluates the performance of RNA-seq measurements in terms of specificity and…

Evaluates the performance of RNA-seq measurements in terms of specificity and sensitivity. Rnaseqcomp is a package that offers several quantitative and visualized benchmarks for RNA-seq…

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DeCoN
Web

DeCoN Developing Cortical Neuron Transcriptome Resource

Enables multidimensional data mining, exploration, and dissemination that is…

Enables multidimensional data mining, exploration, and dissemination that is scalable and designed to integrate future data on additional neuronal classes and different species. DeCoN enables…

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aRNApipe
Desktop

aRNApipe automated RNA-seq pipeline

Provides an integrated and efficient workflow for analyzing single-end and…

Provides an integrated and efficient workflow for analyzing single-end and stranded or unstranded paired-end RNA-seq data. Unlike previous pipelines, aRNApipe is focused on high performance computing…

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Chipster
Desktop

Chipster

A user-friendly analysis software tool for high-throughput data. Chipster…

A user-friendly analysis software tool for high-throughput data. Chipster contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can…

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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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easyRNASeq
Desktop

easyRNASeq

An R package that simplifies the processing of RNA sequencing data, hiding the…

An R package that simplifies the processing of RNA sequencing data, hiding the complex interplay of the required packages behind a single functionality. easyRNASeq calculates the coverage of…

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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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NEUMA
Desktop

NEUMA Normalization by Expected Uniquely Mappable Area

Accurate quantification of transcriptome from RNA-Seq data by effective length…

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization.

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DiffSplice
Desktop

DiffSplice

Detects and visualizes of differential alternative transcription. DiffSplice is…

Detects and visualizes of differential alternative transcription. DiffSplice is an ab initio method to detect alternative splicing isoforms that are differentially expressed under different…

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PennSeq
Desktop

PennSeq

A statistical method that allows each isoform to have its own non-uniform read…

A statistical method that allows each isoform to have its own non-uniform read distribution.

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RUM
Desktop

RUM

An alignment, junction calling, and feature quantification pipeline…

An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

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diffsplicing
Desktop

diffsplicing

A method for ranking the genes and transcripts according to the temporal change…

A method for ranking the genes and transcripts according to the temporal change they show in their expression levels. In order to identify differential splicing and its underlying dynamics, we model…

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SplAdder
Desktop

SplAdder

An alternative splicing toolbox, that takes RNA-Seq alignments and an…

An alternative splicing toolbox, that takes RNA-Seq alignments and an annotation file as input to i) augment the annotation based on RNA-Seq evidence, ii) identify alternative splicing events present…

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GENE-counter
Desktop

GENE-counter

A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for…

A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.

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Corset
Desktop

Corset

A command-line software program to go from a de novo transcriptome assembly to…

A command-line software program to go from a de novo transcriptome assembly to gene-level counts. Corset takes a set of reads that have been multi-mapped to the transcriptome (where multiple…

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PRADA
Desktop

PRADA

A pipeline to analyze paired end RNA-Seq data to generate gene expression…

A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.

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RseqFlow
Desktop

RseqFlow

An RNA-Seq analysis pipeline which offers an express implementation of analysis…

An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.

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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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Rockhopper
Desktop

Rockhopper

A comprehensive and user-friendly system for computational analysis of…

A comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ,…

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CANEapp
Desktop

CANEapp Comprehensive automated Analysis of Next-generation sequencing Experiments

Integrates data from different sources and experiments. CANEapp is a platform…

Integrates data from different sources and experiments. CANEapp is a platform for integrating next-generation sequencing (NGS) analysis pipelines and tools into a user-friendly suite that can be…

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MMSEQ
Desktop

MMSEQ

The package contains a collection of statistical tools for analysing RNA-seq…

The package contains a collection of statistical tools for analysing RNA-seq expression data.

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RNAontheBENCH
Web
Desktop

RNAontheBENCH RNA on the BENCHmark of expression by nCounter hybridisation

Benchmarks RNAseq analysis methods. RNAontheBENCH is a computational resource…

Benchmarks RNAseq analysis methods. RNAontheBENCH is a computational resource that harnesses some features: (i) a RNAseq dataset from 12 human induced pluripotent stem cell lines, (ii) a panel of 150…

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SparseIso
Desktop

SparseIso

Allows identification of isoforms from RNA-seq data. SparseIso is a Bayesian…

Allows identification of isoforms from RNA-seq data. SparseIso is a Bayesian method that considers the reads falling on both splice junctions and exons. In this software, the transcript abundance is…

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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…

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Traph
Desktop

Traph Transcrips in gRAPHs

Allows to identify and quantify transcript. Traph is a de novo genome-based…

Allows to identify and quantify transcript. Traph is a de novo genome-based tool with two-fold advantage: (i) it translates a problem as an established one in the field of network flows, which can be…

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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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EBSeq-HMM
Desktop

EBSeq-HMM

Recognizes genes with non-constant expression over multiple ordered conditions,…

Recognizes genes with non-constant expression over multiple ordered conditions, and simultaneously classify them into expression paths. EBSeq-HMM is based on an empirical Bayes mixture modeling…

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rbamtools
Desktop

rbamtools

A full spectrum of accessibility to BAM for R users are provided such as…

A full spectrum of accessibility to BAM for R users are provided such as reading, writing, extraction of subsets and plotting of alignment depth where the script syntax closely follows the SAM/BAM…

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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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casper
Desktop

casper

Infer alternative splicing from paired-end RNA-seq data. The model is based on…

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start…

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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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systemPipeR
Desktop

systemPipeR

An extensible environment for both building and running end-to-end analysis…

An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique…

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hppRNA
Desktop

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and…

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping,…

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Sequgio
Desktop

Sequgio

Provides an algorithm to estimate isoforms expression from RNA-seq data based…

Provides an algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn't assume uniform distribution of count within transcripts.

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SePIA
Desktop

SePIA Sequence Processing Integration and Analysis

Automates RNA-seq processing, integration and analysis. SePIA allows…

Automates RNA-seq processing, integration and analysis. SePIA allows reproducible analysis of total RNA, poly(A)-derived RNA, small RNA, and integrated microRNA (miRNA) and mRNA data. It provides a…

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zFPKM
Desktop

zFPKM

Determines the expression regime defined by genes controlled by active…

Determines the expression regime defined by genes controlled by active promoters. zFPKM offers a useful data normalization strategy. It can calculate with high consistency the range of gene…

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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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RNA CoMPASS
Desktop

RNA CoMPASS

A web-based GUI distributed computational pipeline, provides all-in-one…

A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the…

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MiTie
Desktop

MiTie Mixed Integer Transcript IdEntification

Offers a framework for transcriptome reconstruction. MiTie starts from a…

Offers a framework for transcriptome reconstruction. MiTie starts from a selection of a set of transcripts for determining and quantifying RNA-Seq-based transcript simultaneously in several samples.…

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TIGAR
Desktop

TIGAR

A sensitive and accurate tool for quantifying transcript isoform abundances…

A sensitive and accurate tool for quantifying transcript isoform abundances from RNA-Seq data. TIGAR2 method performs better than existing methods for the fixed-length reads (100 bp, 250 bp, 500 bp,…

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LFC
Desktop

LFC

An approach to estimate fold changes. LFC is based on a probabilistic model…

An approach to estimate fold changes. LFC is based on a probabilistic model that directly incorporates count ratios instead of read counts. It provides a theoretical foundation for pseudo-counts and…

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Zika-RNAseq-Pip…
Desktop

Zika-RNAseq-Pipeline

Provides an open source RNA-seq processing pipeline that can be used to extract…

Provides an open source RNA-seq processing pipeline that can be used to extract knowledge from any study that profiled gene expression using RNA-seq applied to mammalian cells, comparing two…

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MetaTrans
Desktop

MetaTrans

Analyzes the structure and functions of active microbial communities using the…

Analyzes the structure and functions of active microbial communities using the power of multi-threading computers. MetaTrans is designed to perform two types of RNA-Seq analyses: taxonomic and gene…

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miARma-Seq
Desktop

miARma-Seq

Designed for mRNA, miRNA and circRNA identification and differential expression…

Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different…

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DICEseq
Desktop

DICEseq Dynamic Isoform spliCing Estimator via sequencing data

Determines the dynamics of the splicing isoform proportions from time series…

Determines the dynamics of the splicing isoform proportions from time series RNA-seq data. DICEseq is able to explicitly model correlations between different RNA-seq experiments. It aims to assist…

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TRAP
Desktop
Web

TRAP Time-series RNA-seq Analysis Package

A comprehensive package integrating all necessary tasks such as mapping short…

A comprehensive package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis…

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R-SAP
Desktop

R-SAP

An automated bioinformatics pipeline that analyzes and quantifies…

An automated bioinformatics pipeline that analyzes and quantifies high-throughput RNA-Seq datasets.

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rSeq
Desktop

rSeq

It consists of programs that deal with many aspects of RNA-Seq data analysis,…

It consists of programs that deal with many aspects of RNA-Seq data analysis, such as read quality assessment, sequence mapping, gene and isoform expressions, etc.

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RNA-seq portal
Web

RNA-seq portal

Includes three types of workflows for different tasks. RNA-seq portal permits…

Includes three types of workflows for different tasks. RNA-seq portal permits users to perform computing and analysis, including sequence quality control, read-mapping, transcriptome assembly,…

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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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zUMIs
Desktop

zUMIs

Processes raw reads to count tables for RNA-seq data using Unique Molecular…

Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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DEIsoM
Desktop
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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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Tradict
Desktop

Tradict TRAnscriptome preDICT

Predicts transcriptome-wide gene abundances and the expression of a…

Predicts transcriptome-wide gene abundances and the expression of a comprehensive list of transcriptional programs. Tradict can learn and use the expression measurements of a small subset of 100…

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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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TRUFA
Web

TRUFA TRanscriptome User-Friendly Analysis

Offers a web-based interface that generates the outputs commonly used in de…

Offers a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing…

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tximport
Desktop

tximport

Helps users integrate transcript-level abundance estimates from common…

Helps users integrate transcript-level abundance estimates from common quantification pipelines into count-based statistical inference engines. tximport imports transcript lengths and abundance…

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WemIQ
Desktop
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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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TCW
Desktop

TCW Transcriptome Computational Workbench

A software package for assembling, annotating, querying, and comparing…

A software package for assembling, annotating, querying, and comparing transcript and expression level 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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DeTCT
Desktop

DeTCT Differential expression Transcript Counting Technique

A purely quantitative digital gene expression sample processing and analysis…

A purely quantitative digital gene expression sample processing and analysis package. DeTCT begins with tissue samples and produces a text table or HTML table, comprising genomic coordinates…

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QuickNGS
Desktop
Web

QuickNGS

A workflow system for laboratories with the need to analyze data from multiple…

A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and…

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NURD
Desktop

NURD

A software which accurately estimates isoform level expression from RNA-seq…

A software which accurately estimates isoform level expression from RNA-seq data. It uses a binary interval search algorithm and can correct both the global tendency of sequencing bias in the data…

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Glbase
Desktop

Glbase

Allows the user to perform many common analyses on ChIP-seq, microarray and…

Allows the user to perform many common analyses on ChIP-seq, microarray and RNA-seq data. Glbase is a flexible and multifunctional toolkit which includes many functions to intersect two lists of…

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IRAP
Desktop

IRAP integrated RNA-seq Analysis Pipeline

A flexible RNA-seq analysis pipeline that allows the user to select and apply…

A flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression and testing for differential…

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Isolator
Desktop

Isolator

A versatile model to account for sequence specific bias that commonly occurs at…

A versatile model to account for sequence specific bias that commonly occurs at the ends of fragments. Isolotar analyzes RNA-Seq experiments using a simple Bayesian hierarchical model. Combined with…

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BENTO-Seq
Desktop

BENTO-Seq

A Python implementation of the positional bootstrap algorithm which quantifies…

A Python implementation of the positional bootstrap algorithm which quantifies the level of uncertainty in expression induced by nonuniform coverage. Unlike methods that attempt to correct for biases…

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CLASS
Desktop

CLASS Constraint-based Local Assembly and Selection of Splice variants

Identifies low abundance splice variation with high accuracy. CLASS employs a…

Identifies low abundance splice variation with high accuracy. CLASS employs a linear programming method to detect exons. It can select candidate transcripts using an efficient dynamic programming…

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READemption
Desktop

READemption

Permits the computational evaluation of RNA-Seq data. READemption is an…

Permits the computational evaluation of RNA-Seq data. READemption is an automated RNA-Seq processing with the initial purpose to handle differential RNA-Seq (dRNA-Seq) data for the determination of…

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PDEGEM
Desktop

PDEGEM Positional Dependent Energy Guided Expression Model

Estimates the abundance of transcripts. PDEGEM can improve the accuracy in…

Estimates the abundance of transcripts. PDEGEM can improve the accuracy in modeling and estimating the transcript abundance and isoform expression in RNA-Seq data. Additionally, although the stacking…

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OncoRep
Desktop

OncoRep Oncogenomics Report

A fully automated RNA-Seq based report for patients with (breast) cancer, which…

A fully automated RNA-Seq based report for patients with (breast) cancer, which includes molecular classification, detection of altered genes, detection of altered pathways, identification of gene…

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Guide
Desktop

Guide

A desktop application for the bench biologists to analyse RNA-Seq and…

A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data.

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NLDMseq
Desktop

NLDMseq

Provides an approach to accurately estimate gene and isoform expression from…

Provides an approach to accurately estimate gene and isoform expression from RNA-seq data by modeling the isoform- and exon-specific read sequencing biases. NLDMseq makes use of a latent variable…

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EMSAR
Desktop

EMSAR Estimation by Mappability-based Segmentation And Reclustering

An approach for quantifying transcript abundance from RNA-seq data. EMSAR…

An approach for quantifying transcript abundance from RNA-seq data. EMSAR groups reads according to the set of transcripts to which they are mapped and finds maximum likelihood estimates using a…

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IAOseq
Desktop

IAOseq

A software tool that is based on reads distributions along the transcribed…

A software tool that is based on reads distributions along the transcribed regions to identify the expression levels of overlapping genes from standard RNA-seq data. Compared with five commonly used…

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rnaSeqMap
Desktop

rnaSeqMap

A toolbox for analyses that may be performed with the use of gene annotations…

A toolbox for analyses that may be performed with the use of gene annotations or alternatively, in an unsupervised mode, on any genomic region to find novel or non-standard transcripts. The data…

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IQSeq
Desktop

IQSeq

Integrated Isoform Quantification Analysis based on A Partial Sampling…

Integrated Isoform Quantification Analysis based on A Partial Sampling Framework.

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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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r-make
Desktop

r-make

A pipeline that processes RNA sequencing reads. r-make estimates the expression…

A pipeline that processes RNA sequencing reads. r-make estimates the expression levels for exons, genes, and splice junctions. In the process, it prints a range of quality metrics and statistics,…

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miRProf
Desktop

miRProf miRNA Profiler

Determines normalised expression levels of sRNAs matching known miRNAs in…

Determines normalised expression levels of sRNAs matching known miRNAs in miRBase. miRProf can compare miRNA expression levels across multiple samples. It filters sRNA sequences in each sample before…

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POME
Desktop

POME Poisson mixed-effects

A model to characterize base-level read coverage within each transcript. The…

A model to characterize base-level read coverage within each transcript. The underlying expression level is included as a key parameter in this model. Since the proposed model is capable of…

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RSEQtools
Desktop

RSEQtools

A suite of tools that use this format for the analysis of RNA-Seq experiments.

A suite of tools that use this format for the analysis of RNA-Seq experiments.

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BADGE
Desktop

BADGE

A Bayesian hierarchical approach to investigate within-sample and…

A Bayesian hierarchical approach to investigate within-sample and between-sample variations in RNA-Seq data.

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rpkmforgenes.py
Desktop

rpkmforgenes.py

Calculates gene expression for RNA-Seq data. By default, rpkmforgenes.py…

Calculates gene expression for RNA-Seq data. By default, rpkmforgenes.py ignores 3' untranslated regions.

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Mix2
Desktop

Mix2

Uses a mixture of probability distributions to model the transcript specific…

Uses a mixture of probability distributions to model the transcript specific positional fragment bias.

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dsPIG
Desktop

dsPIG deep sequencing-based Prediction of Imprinted Genes

Identifies imprinted genes with high sensitivity and specificity and a low…

Identifies imprinted genes with high sensitivity and specificity and a low false discovery rate (FDR) when the number of sequenced tissue samples was fairly large. dsPIG is a Bayesian model which…

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TEMT
Desktop

TEMT Transcript Estimation from Mixed Tissue samples

A probabilistic model-based approach to estimate the transcript abundances of…

A probabilistic model-based approach to estimate the transcript abundances of each cell type of interest from RNA-seq data of heterogeneous tissue samples. TEMT incorporates positional and…

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RD
Desktop

RD

This R package is intended to implement a program for statistical estimation of…

This R package is intended to implement a program for statistical estimation of isoform expression levels using RNA-Seq based on the modeling of RNA degradation. This method can improve the accuracy…

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SEQ-EM
Desktop

SEQ-EM

A rigorous alternative for handling the reads generated in an RNA-seq…

A rigorous alternative for handling the reads generated in an RNA-seq experiment within a probabilistic model for RNA-seq data; A maximum likelihood-based methods for estimating the model parameters…

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Hera
Desktop

Hera

Helps to analyze RNA-seq data. Hera is a bioinformatics software that provides…

Helps to analyze RNA-seq data. Hera is a bioinformatics software that provides (i) base-to-base alignment BAM file, (ii) transcript abundance estimation, and (iii) fusion gene detection with fused…

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DuffyRNAseq
Desktop

DuffyRNAseq

Implements an analysis pipeline for processing RNA-seq data from Illumina…

Implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression. DuffyRNAseq offers a multistep read assignment…

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DEB
Web

DEB

Automates all the steps in file preparation, computation and result comparison.…

Automates all the steps in file preparation, computation and result comparison. DEB is an online pipeline that integrates three algorithms into one place: (i) EdgeR designed for the analysis of…

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Partek Flow
Desktop

Partek Flow

Enable researchers to self-sufficiently perform data analysis. Partek Flow…

Enable researchers to self-sufficiently perform data analysis. Partek Flow software is designed specifically for the analysis needs of next generation sequencing (NGS) applications including RNA,…

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AIR
Web

AIR Artificial intelligence RNAseq

Offers a solution to close the gap between data production and data…

Offers a solution to close the gap between data production and data interpretation, making it possible for researchers to do their own analysis in the simplest possible way and giving them the…

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CLRNASeq
Desktop

CLRNASeq

A robust standalone software developed specifically for discovering, profiling…

A robust standalone software developed specifically for discovering, profiling and quantifying RNA transcripts. With an intuitive interface and point and click menu options, users are given the power…

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qRNASeq script
Desktop

qRNASeq script

Bioo Scientific offers a complementary qRNASeq script, which eliminates PCR…

Bioo Scientific offers a complementary qRNASeq script, which eliminates PCR duplicates from RNA-Seq data when Molecular Indexes™ or other stochastic adapters are used during library prep. Using…

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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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INSEGT
Desktop

INSEGT INtersecting SEcond Generation sequencing daTa with annotation

A tool to analyse alignments of RNA-Seq reads (single-end or paired-end) by…

A tool to analyse alignments of RNA-Seq reads (single-end or paired-end) by using gene annotations. INSEGT can measure exon, transcript and gene expression levels of given annotations. If read…

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QRNAseq
Desktop

QRNAseq

A tool to manage huge amounts of RNA-seq data in an integrative way which…

A tool to manage huge amounts of RNA-seq data in an integrative way which includes RNA-seq data quality control, read alignment, gene fusion, gene mutation, isoform identification and function…

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TranSEQ
Desktop

TranSEQ

Aims to estimate the mRNA expression levels of alternatively spliced…

Aims to estimate the mRNA expression levels of alternatively spliced transcripts from the next-generation mRNA sequencing data. The program takes the mRNA sequencing data and the candidate mRNA…

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ISP
Desktop

ISP

Accurate inference of isoforms from multiple samples RNA-Seq data. ISP is…

Accurate inference of isoforms from multiple samples RNA-Seq data. ISP is written in C++ and can be run on Linux/Unix systems.

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Tuxedo
Desktop

Tuxedo

Handles RNA-sequencing pipeline that is based on TopHat suite. The Tuxedo…

Handles RNA-sequencing pipeline that is based on TopHat suite. The Tuxedo protocol allows to assess alternative splicing inferred on fragments per kilobase per million (FPKM) values.

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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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SeqExpress
Desktop

SeqExpress

Evaluates isoform or gene expression level. SeqExpress is a standalone software…

Evaluates isoform or gene expression level. SeqExpress is a standalone software for furnishing an accurate estimation thanks to the investigating of the sequencing bias from mRNA-Seq data.

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CLIIQ
Desktop

CLIIQ

An algorithm to simultaneously identify and quantify expressed isoforms based…

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

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bcbio-nextgen
Desktop

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

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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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ERANGE
Desktop

ERANGE Enhanced Read Analysis of Gene Expression

A software tool for mapping and quantifying Mammalian transcriptomes by…

A software tool for mapping and quantifying Mammalian transcriptomes by RNA-Seq. The functions of ERANGE are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads…

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RobiNA
Desktop

RobiNA

A User Friendly Graphical Interface to Powerful Open Source Microarray and…

A User Friendly Graphical Interface to Powerful Open Source Microarray and RNA-Seq Processing.

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MaxInfo
Desktop

MaxInfo

Allows identification and quantification of isoforms based on information…

Allows identification and quantification of isoforms based on information coding theory. MaxInfo considers isoforms and reads as the ‘signal sources’ and ‘short codes’ of an information…

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FX
Desktop

FX

A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept…

A user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.

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IsoformEx
Desktop

IsoformEx

A fast and accurate algorithm to estimate transcript expression levels and gene…

A fast and accurate algorithm to estimate transcript expression levels and gene expression levels, which takes into account short exons and alternative exons with a weighting scheme. IsoformEx…

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Artemis
Desktop

Artemis