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Novel isoform quantification software tools | RNA-seq analysis

RNA-Seq is being increasingly adopted as the technology of choice for gene expression studies, and with large numbers of experiments producing partial transcripts of genes, it is expected that there will be rapid progress in the coming years in…
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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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Scripture
Desktop

Scripture

A method for transcriptome reconstruction that relies solely on RNA-Seq reads…

A method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage…

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StringTie
Desktop

StringTie

A fast and highly efficient assembler of RNA-Seq alignments into potential…

A fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de…

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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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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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SplitSeek
Desktop

SplitSeek

Identifies splice junctions. SplitSeek allows de novo prediction of splice…

Identifies splice junctions. SplitSeek allows de novo prediction of splice junctions in short-read RNA-seq data. The software consists of two programs that are executed sequentially. It can detect…

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iReckon
Desktop

iReckon

An algorithm for the simultaneous isoform reconstruction and abundance…

An algorithm for the simultaneous isoform reconstruction and abundance estimation.

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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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CIDANE
Desktop

CIDANE Comprehensive Isoform Discovery and AbuNdance Estimation

A framework for genome-based transcript reconstruction and quantification.…

A framework for genome-based transcript reconstruction and quantification. CIDANE is engineered to not only assembly RNA-seq reads ab initio, but to also make use of the growing annotation of known…

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UnoSeq
Desktop

UnoSeq

A Java library to analyze next generation sequencing data and especially…

A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.

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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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FlipFlop
Desktop

FlipFlop

Implements a fast method for de novo transcript discovery and abundance…

Implements a fast method for de novo transcript discovery and abundance estimation from RNA-seq data. FlipFlop differs from Cufflinks by simultaneously performing the identification and quantitation…

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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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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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CEM
Desktop

CEM

An algorithm to assemble transcripts and estimate their expression levels from…

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

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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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Oqtans
Desktop

Oqtans Online quantitative transcriptome analysis

It is based on the Galaxy-framework and provides tools for read mapping,…

It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.

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ORMAN
Desktop

ORMAN Optimal Resolution of Multimapping Ambiguity of RNA-Seq Reads

Aims to compute the minimum number of potential transcript products for each…

Aims to compute the minimum number of potential transcript products for each gene and to assign each multimapping read to one of these transcripts based on the estimated distribution of the region…

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IsoLasso
Desktop

IsoLasso

An algorithm used to assemble transcripts and estimate their expression levels…

An algorithm used to assemble transcripts and estimate their expression levels from RNA-Seq reads. Three mains goals are reached by IsoLasso: the maximization of prediction accuracy, minimization of…

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LocExpress
Web

LocExpress

Provides nearly real-time expression estimation for novel transcripts in common…

Provides nearly real-time expression estimation for novel transcripts in common tissues and cell types. LocExpress is a web server for efficiently estimating expression of novel transcripts across…

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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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NMFP
Desktop

NMFP Non-negative Matrix Factorization Preselection

A preselection method which is designed to improve the accuracy of…

A preselection method which is designed to improve the accuracy of computational methods in identifying mRNA isoforms from RNA-seq data. Through simulation and real data studies, NMFP can effectively…

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SLIDE
Desktop

SLIDE

We have developed a statistical method that takes exon boundaries and RNA-Seq…

We have developed a statistical method that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample.

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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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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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NSMAP
Desktop

NSMAP Nonnegativity and Sparsity constrained Maximum A Posteriori

Provides a method for identifying and evaluating expression levels of isoforms…

Provides a method for identifying and evaluating expression levels of isoforms from RNA-Seq data. NSMAP is a statistical model for RNA-Seq data analysis which can be used without annotations from…

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RNA-Rocket
Web

RNA-Rocket

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for…

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the…

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SAMMate
Desktop

SAMMate

An open source GUI software suite to process RNA-Seq data. It is composed of…

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate. assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA…

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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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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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deGPS
Desktop

deGPS

A powerful and robust tool for data normalization and detecting different…

A powerful and robust tool for data normalization and detecting different expression in RNA-seq experiments. deGPS contains new normalization methods based on generalized Poisson distribution…

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RAP
Web

RAP RNA-seq Analysis Pipeline

Allows users to analyze sequencing data in multiple steps. The RAP purpose is…

Allows users to analyze sequencing data in multiple steps. The RAP purpose is to investigate the complex transcriptional landscape of eukaryotic transcriptomes through a computationally optimized…

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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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Strawberry
Desktop

Strawberry

Serves for transcript reconstruction and quantification from paired-end RNA-seq…

Serves for transcript reconstruction and quantification from paired-end RNA-seq data. Strawberry simplifies discovery of novel isoforms and calculation of transcript-level expression. It can process…

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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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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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Astroid
Desktop

Astroid

An algorithm that simultaneously reconstruct transcripts and estimate their…

An algorithm that simultaneously reconstruct transcripts and estimate their abundance. The program takes read alignment as input in SAM format, and provides reconstructed transcripts in the standard…

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DRUT
Desktop

DRUT

Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated…

Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data.

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outrigger
Desktop

outrigger

Uses junction reads from RNA seq data, and a graph database to create a de novo…

Uses junction reads from RNA seq data, and a graph database to create a de novo alternative splicing annotation with a graph database. Outrigger is a Python package and an RNA-seq analysis software…

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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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IsoInfer
Desktop

IsoInfer

Infers isoforms from short RNA-Seq reads and information concerning exon-intron…

Infers isoforms from short RNA-Seq reads and information concerning exon-intron boundaries and transcription start site (TSS) - poly-A site (PAS) pairs. IsoInfer can calculate the expression levels…

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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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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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MaLTA
Desktop

MaLTA

A method for simultaneous transcriptome assembly and quantification from Ion…

A method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data. This approach explores transcriptome structure and incorporates a maximum likelihood model into the…

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ReXpress
Desktop

ReXpress

An efficient algorithm for updating abundance estimates from RNA-Seq…

An efficient algorithm for updating abundance estimates from RNA-Seq experiments on re-annotation that does not require re-analysis of the entire dataset. This approach is based on a fast…

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