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Differential expression software tools | RNA sequencing data analysis

One of the main goals of RNA-seq experiments is to identify the differentially expressed genes in two or more conditions. Such genes are selected based on a combination of expression change threshold and score cutoff, which are usually based on P…
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DESeq
Desktop

DESeq

A method for differential analysis of RNA-sequencing count data, using…

A method for differential analysis of RNA-sequencing count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a…

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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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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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Ballgown
Desktop

Ballgown

A software package designed to facilitate flexible differential expression…

A software package designed to facilitate flexible differential expression analysis of RNA-Seq data. Ballgown can also be used to visualize the transcript assembly on a gene-by-gene basis, extract…

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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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NOISeq
Desktop

NOISeq

Identifies differentially expressed genes from count data or previously…

Identifies differentially expressed genes from count data or previously normalized count data. NOISeq empirically models the noise distribution of count changes by contrasting fold-change differences…

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DEGseq
Desktop

DEGseq

A package to identify differentially expressed genes or isoforms for RNA-seq…

A package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. DEGseq also encourage users to export gene expression values in a table format which could be…

limma
Desktop

limma Linear Models for Microarray Data

Provides an integrated solution for analysing data from gene expression…

Provides an integrated solution for analysing data from gene expression experiments. limma contains rich features for handling complex experimental designs and for information borrowing to overcome…

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ALDEx
Desktop

ALDEx ANOVA-Like Differential Expression

An ANOVA-like differential expression procedure, to identify genes with greater…

An ANOVA-like differential expression procedure, to identify genes with greater between condition differences. ALDEx is the only method capable of producing an estimate of the ratio of…

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DSS-single
Desktop

DSS-single

A package based on a statistical method for detecting DMRs from WGBS (Whole…

A package based on a statistical method for detecting DMRs from WGBS (Whole Genome Bisulfite Sequencing) data without replicates. A key feature of DSS-single is to estimate biological variation when…

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derfinder
Desktop

derfinder

Improves the annotation-agnostic approach to RNA-seq analysis by: (1)…

Improves the annotation-agnostic approach to RNA-seq analysis by: (1) implementing a computationally efficient bump-hunting approach to identify DERs which permits genome-scale analyses in a large…

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EBSeq
Desktop

EBSeq

Identifies differentially expressed (DE) isoforms in RNA-seq experiments. EBSeq…

Identifies differentially expressed (DE) isoforms in RNA-seq experiments. EBSeq is a R package, based on a parametric mixture model, that facilitates evaluation of the posterior probabilities…

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baySeq
Desktop

baySeq

Recognizes differential expression in RNA-seq data using a negative binomial…

Recognizes differential expression in RNA-seq data using a negative binomial distribution. baySeq is based on a parametric empirical Bayes point estimation method and an empirical Bayesian approach.…

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Myrna
Desktop

Myrna

A cloud computing tool for calculating differential gene expression in large…

A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization,…

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JuncBASE
Desktop

JuncBASE

It is used to identify and classify alternative splicing events from RNA-Seq…

It is used to identify and classify alternative splicing events from RNA-Seq data.

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edgeR-robust
Desktop

edgeR-robust

Dampens the effect of outliers on count-based differential expression analyses.…

Dampens the effect of outliers on count-based differential expression analyses. A strategy based on observation weights that can be used within existing frameworks.

Babelomics
Desktop
Web

Babelomics

A web application for the functional analysis of gene expression and genomic…

A web application for the functional analysis of gene expression and genomic data. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a…

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SeqGSEA
Desktop

SeqGSEA

Provides methods for gene set enrichment analysis of high-throughput RNA-Seq…

Provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data,…

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sRNAtoolbox
Web

sRNAtoolbox

A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small…

A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and…

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BBSeq
Desktop

BBSeq

Provides an approach for RNA-Seq transcriptional count data analysis. BBSeq is…

Provides an approach for RNA-Seq transcriptional count data analysis. BBSeq is a R package that aims to offer a simplified software for modeling and building design matrices with an automatic…

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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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NSVA
Desktop

NSVA Nonnegative Singular Value Approximation

Enhances RNA-seq analysis by taking advantages of RNA-seq data’s built-in…

Enhances RNA-seq analysis by taking advantages of RNA-seq data’s built-in non-negativity. NSVA can contribute to enhancing data locality and capturing latent data behavior. It selects genes…

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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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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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DEIVA
Web
Desktop

DEIVA Differential Gene Expression Interactive Visual Analysis

Enables locating and identifying single or multiple genes in an immediate,…

Enables locating and identifying single or multiple genes in an immediate, interactive, and intuitive manner. DEIVA offers a unique combination of design decisions that enable inspection and analysis…

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sSeq
Desktop

sSeq

The purpose of this package is to discover the genes that are differentially…

The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments.

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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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PANDORA
Desktop

PANDORA PerformANce Driven scOring of RNA-Seq stAtistics

Analyzes RNA-Seq gene expression data. PANDORA provides an intuitive…

Analyzes RNA-Seq gene expression data. PANDORA provides an intuitive methodology for the optimization of statistical accuracy and agreement between alternative transcriptional measurements. It is…

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DEXUS
Desktop

DEXUS

Identifies differentially expressed transcripts in RNA-Seq data with unknown…

Identifies differentially expressed transcripts in RNA-Seq data with unknown conditions. DEXUS models read counts as a finite mixture of negative binomial distributions in which each mixture…

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ROTS
Desktop

ROTS Reproducibility-Optimized Test Statistic

An R package for ranking genes or proteins in terms of differential expression…

An R package for ranking genes or proteins in terms of differential expression in two-group comparisons. The procedure selects a ranking statistic from a family of t-type statistics by maximizing the…

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SDEAP
Desktop

SDEAP

A differential transcript expression (DTE) analysis algorithm. SDEAP estimates…

A differential transcript expression (DTE) analysis algorithm. SDEAP estimates the number of conditions directly from the input samples using a Dirichlet mixture model and discovers alternative…

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ImpulseDE
Desktop

ImpulseDE

Captures single impulse-like progression patterns in high throughput time…

Captures single impulse-like progression patterns in high throughput time series datasets. ImpulseDE can be applied on any kind of high throughput gene expression data. It reports differentially…

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TCC
Desktop

TCC Tag Count Comparison

Allows users to perform differential expression (DE) analysis of tag count…

Allows users to perform differential expression (DE) analysis of tag count data. The Tag Count Comparison purpose is to reduce potential differentially expressed genes (DEGs) before performing the…

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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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rDiff
Desktop

rDiff

An open source tool for accurate detection of differential RNA processing from…

An open source tool for accurate detection of differential RNA processing from RNA-Seq data.

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SAMSeq
Desktop

SAMSeq

A nonparametric approach for identifying differential expression in RNA-Seq…

A nonparametric approach for identifying differential expression in RNA-Seq data.

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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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QuasiSeq
Desktop

QuasiSeq

Analyses RNA sequencing count tables using quasi-likelihood. QuasiSeq is used…

Analyses RNA sequencing count tables using quasi-likelihood. QuasiSeq is used to apply the QL, QLShrink and QLSpline methods to quasi-Poisson or quasi-negative binomial models for identifying…

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ABSSeq
Desktop

ABSSeq ABSolute differences of RNA-Seq data

A RNA-Seq analysis method based on modelling absolute expression differences.…

A RNA-Seq analysis method based on modelling absolute expression differences. ABSSeq infers differential gene expression (DE) through the absolute differences in gene expression and assumes the…

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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.

TEtools
Desktop

TEtools transposable elements tools

Provides analysis of TE expression. TEtools takes into account the TE sequence…

Provides analysis of TE expression. TEtools takes into account the TE sequence diversity of the genome. It can be applied to unannotated or unassembled genomes and is freely available under the GPL3.…

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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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SigFuge
Desktop

SigFuge

Tests significance of clustering in RNA-seq data. SigFuge allows to identify…

Tests significance of clustering in RNA-seq data. SigFuge allows to identify genomic loci exhibiting differential transcription patterns across many RNA-seq samples. It combines clustering with…

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LPEseq
Desktop

LPEseq Local-Pooled-Error with RNA-sequencing data

Interprets differential expression (DE) detection of RNA-Seq experiments with a…

Interprets differential expression (DE) detection of RNA-Seq experiments with a small number or non-replicated samples in each class. LPEseq evaluates the baseline error distribution for each of the…

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jGRP
Desktop

jGRP

Identifies differentially expressed genes. jGRP is a transcriptomic data…

Identifies differentially expressed genes. jGRP is a transcriptomic data meta-analysis method. It integrates multiple gene expression data sets in a gene regulatory space instead of in the original…

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SEGtool
Desktop

SEGtool specifically expressed gene tool

Permits the detection of specifically expressed genes (SEGs) from numeric gene…

Permits the detection of specifically expressed genes (SEGs) from numeric gene expression data. SEGtool is based on modified fuzzy c-means (FCM), Jaccard index and greedy annealing methods. It is…

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Linnorm
Desktop

Linnorm

Provides a linear model and normality based transformation method. Linnorm is…

Provides a linear model and normality based transformation method. Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIPseq count data or any large-scale count data. It transforms such…

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SeqMADE
Desktop

SeqMADE

Serves to the RNA-seq differential expression analysis. SeqMADE implements…

Serves to the RNA-seq differential expression analysis. SeqMADE implements within a well-established generalized linear model framework integrating gene expression into the network module, instead of…

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EEGC
Desktop

EEGC Engineering Evaluation by Gene Categorization

Evaluates cellular engineering processes in a systemic rather than marker-based…

Evaluates cellular engineering processes in a systemic rather than marker-based fashion. EEGC integrates transcriptome profiling and functional analysis. It clusters genes into categories…

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tcgsaseq
Desktop

tcgsaseq

Applies to virtually all RNA-seq study designs, including traditional…

Applies to virtually all RNA-seq study designs, including traditional case-control and more complex studies. tcgsaseq is a principled, model-free and efficient top-down method for detecting…

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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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edgeRun
Desktop

edgeRun

An R package that implements an unconditional exact test that is a more…

An R package that implements an unconditional exact test that is a more powerful version of the exact test in edgeR. This increase in power is especially pronounced for experiments with as few as 2…

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pathDESeq
Desktop

pathDESeq

Allows to reduce false discovery rates (FDRs). pathDESeq is a statistical…

Allows to reduce false discovery rates (FDRs). pathDESeq is a statistical method that uses known biological pathways and interaction to cut FDRs. To find differentially expressed (DE), this tool uses…

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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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variancePartiti…
Desktop

variancePartition

Enables rapid interpretation of complex gene expression studies as well as…

Enables rapid interpretation of complex gene expression studies as well as other high-throughput genomics assays. variancePartition is a statistical and visualization framework, used to prioritize…

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timeSeq
Desktop

timeSeq

Detectes the differentially expressed (DE) genes in time course RNA-Seq data.…

Detectes the differentially expressed (DE) genes in time course RNA-Seq data. The negative binomial mixed-effect model (NBMM) method is applied to gene expression data on a gene-by-gene basis. A…

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multiDE
Desktop

multiDE

Facilitates the differential expression (DE) analysis of RNA-seq read count…

Facilitates the differential expression (DE) analysis of RNA-seq read count data generated by experiments with multiple conditions, which takes the correlation between samples into account. multiDE…

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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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Key…
Desktop

Key ingredients Differential Analysis RNAseq

Assess the impact of the key components of the statistical framework for…

Assess the impact of the key components of the statistical framework for differential analyses of RNA-seq data. This tool is based on real data sets and allows the exploration of various scenarios…

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ELTSeq
Desktop

ELTSeq

Detects differentially expressed (DE) genes for RNA-seq data with high level of…

Detects differentially expressed (DE) genes for RNA-seq data with high level of heterogeneity such as cancer RNA-seq data. ELTSeq is an empirical likelihood ratio test (ELT) with a mean-variance…

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tweeDEseq
Desktop

tweeDEseq

Differential expression analysis of RNA-seq using the Poisson-Tweedie family of…

Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

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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…

Eoulsan
Desktop

Eoulsan

A versatile framework based on the Hadoop implementation of the MapReduce…

A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.

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Cyber-T
Web
Desktop

Cyber-T

Provides differential analysis tools for high-throughput data. Cyber-T handles…

Provides differential analysis tools for high-throughput data. Cyber-T handles many types of data, from DNA and Protein microarrays, to Next Generation Sequencing (NGS), to Quantitative Mass…

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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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Plastid
Desktop

Plastid

Allows users to analyze nucleotide-resolution of genomics data. Plastid can…

Allows users to analyze nucleotide-resolution of genomics data. Plastid can extract the relevant biological information from various properties of raw read alignments. It provides consistent…

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RNAMiner
Web

RNAMiner

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five…

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed…

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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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BayesMetaSeq
Desktop

BayesMetaSeq

A Bayesian hierarchical model for RNA-seq meta-analysis and biomarker…

A Bayesian hierarchical model for RNA-seq meta-analysis and biomarker categorization by study heterogeneity. BayesMetaSeq models the RNA-seq count data and integrates information across genes and…

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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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sleuth
Desktop

sleuth

A statistical method for the differential analysis of RNA-Seq data that…

A statistical method for the differential analysis of RNA-Seq data that utilizes bootstrapping in conjunction. sleuth is able to improve on traditional count-based methods by utilizing improved…

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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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samExploreR
Desktop

samExploreR

An R package that allows the subsampling (m out of n bootstraping) of…

An R package that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design.…

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contamDE
Desktop

contamDE

Conducts differential expression (DE) analysis using high throughput…

Conducts differential expression (DE) analysis using high throughput next-generation RNA-seq read count data generated from contaminated tumor samples that are either matched or unmatched with normal…

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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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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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RNAseqDifferent…
Desktop

RNAseqDifferentialExpression

Uses for RNA-Seq analysis. RNAseqDifferentialExpression is a script for running…

Uses for RNA-Seq analysis. RNAseqDifferentialExpression is a script for running code of analysis tool. The choice of RNA-Seq analysis workflow, applied to genotypically heterogeneous samples, exerts…

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ASC
Desktop

ASC Analysis of Sequence Counts

Borrows information across sequences to establish prior distribution of sample…

Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available.

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MRFSEQ
Desktop

MRFSEQ

A new efficient algorithm based on a Markov random field (MRF) model that uses…

A new efficient algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance the prediction power.

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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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XBSeq
Desktop

XBSeq

Allows users to test differential expression of RNA-seq, where non-exonic…

Allows users to test differential expression of RNA-seq, where non-exonic mapped reads are used to model background noise for RNA-seq. XBSeq provides functionality to directly process alignment files…

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INDEED
Algorithm

INDEED Integrated DiffErential Expression and Differential network analysis

Builds a sparse differential network based on partial correlation for better…

Builds a sparse differential network based on partial correlation for better visualization, and integrates differential expression (DE) and differential network (DN) analyses for biomarker discovery.…

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iFad
Desktop

iFad

An R package implementing a bayesian sparse factor model for the joint analysis…

An R package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g.…

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DSGseq
Desktop

DSGseq

This program is aimed to identify differentially spliced genes from two groups…

This program is aimed to identify differentially spliced genes from two groups of RNA-seq samples.

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SARTools
Desktop

SARTools Statistical Analysis of RNA-Seq data Tools

An R package dedicated to the differential analysis of RNA-seq data. SARTools…

An R package dedicated to the differential analysis of RNA-seq data. SARTools provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well-known…

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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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iDEP
Web
Desktop

iDEP Integrated Differential Expression and Pathway analysis

Analyzes gene expression data from DNA microarray or RNA-Seq. iDEP integrates…

Analyzes gene expression data from DNA microarray or RNA-Seq. iDEP integrates many commonly-used R/Bioconductor packages with comprehensive annotation databases. Normalized expression and RNA-Seq…

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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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MDSeq
Desktop

MDSeq

Allows to analyze large-scale RNA-seq studies. MDSeq utilizes a novel…

Allows to analyze large-scale RNA-seq studies. MDSeq utilizes a novel re-parametrization of the negative binomial to permit for robust statistical inference and efficient computations of the…

WoPPER
Web
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RNA-seq 2G
Web

RNA-seq 2G

Uses read count data from RNA-seq or similar data matrix as input and generates…

Uses read count data from RNA-seq or similar data matrix as input and generates test statistics in consistent format as output. RNA-seq 2G is a web portal with over 25 statistical methods that…

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DEApp
Web

DEApp

Enables models selection, parameter tuning, cross validation and visualization…

Enables models selection, parameter tuning, cross validation and visualization of results in a user-friendly interface. DEApp is an interactive and dynamic web application for differential expression…

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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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viGEN
Desktop

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and…

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first…

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TCGA_RNASeq_Cli…
Desktop

TCGA_RNASeq_Clinical

This repository includes code for processing RNA-Seq FASTQ files and clinical…

This repository includes code for processing RNA-Seq FASTQ files and clinical data from The Cancer Genome Atlas. This pipeline is designed to be executed on Unix-based systems. Most of the code is…

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TEToolkit
Desktop

TEToolkit

A method and software package for including both gene- and TE-associated…

A method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. TEtranscripts shows improved recovery of TE transcripts over…

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rSeqNP
Desktop

rSeqNP

Implements a non-parametric approach to test for differential expression and…

Implements a non-parametric approach to test for differential expression and splicing from RNA-Seq data. rSeqNP uses permutation tests to access statistical significance and can be applied to a…

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GMD
Desktop

GMD Generalized Minimum Distance of distributions

An R package to assess the similarity between spatial distributions of…

An R package to assess the similarity between spatial distributions of read-based sequencing data such as ChIP-seq and RNA-seq. GMD calculates the optimal distance between pairs of normalized signal…

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GFOLD
Desktop

GFOLD Generalized fold change

Produces biologically meaningful rankings of differentially expressed genes…

Produces biologically meaningful rankings of differentially expressed genes from RNA-seq data. GFOLD assigns reliable statistics for expression changes based on the posterior distribution of log fold…

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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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Rcount
Desktop

Rcount

Allows the user to assign priorities to certain feature types (e.g. higher…

Allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions. Rcount provides a fast and…

DiscriminantCut
Desktop

DiscriminantCut

Explores the linear decision boundary family. DiscriminantCut is a machine…

Explores the linear decision boundary family. DiscriminantCut is a machine learning methodology for robust differential expression analysis, which can be an avenue to significantly advance research…

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NBLDA
Desktop

NBLDA Negative Binomial Linear Discriminant Analysis

A negative binomial linear discriminant analysis for RNA-Seq data. NBLDA was…

A negative binomial linear discriminant analysis for RNA-Seq data. NBLDA was constructed by fitting a negative binomial model, and proposed some plug-in rules to estimate the unknown parameters in…

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rSeqDiff
Desktop

rSeqDiff

An R package that can detect differential gene and isoform expressions from…

An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions.

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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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MutRSeq
Desktop

MutRSeq

A statistical method for detecting differentially expressed single nucleotide…

A statistical method for detecting differentially expressed single nucleotide variants (SNVs) based on RNA-seq data. Specifically, we focus on nonsynonymous mutations and employ a hierarchical…

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ShrinkBayes
Desktop

ShrinkBayes

A method for detecting differential features across the entire spectrum,…

A method for detecting differential features across the entire spectrum, including the lower counts.

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RNASeqGUI
Desktop

RNASeqGUI

A graphical user interface that helps biologists to handle and analyse large…

A graphical user interface that helps biologists to handle and analyse large data collected in RNA-seq experiments. The novel version of RNASeqGUI combines graphical interfaces with tools for…

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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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EpiCenter
Desktop

EpiCenter

A powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting…

A powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting differentially expressed genes or identifying changes in epigenetic modifications (histone acetylation/methylation…

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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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DEAR-O
Web

DEAR-O Differential Expression Analysis based on RNA-seq data – Online

A user-friendly platform for performance evaluation of differential expression…

A user-friendly platform for performance evaluation of differential expression analysis based on RNA-seq data. DEAR-O currently includes four of the most popular tools: DESeq, DESeq2, edgeR and…

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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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compcodeR
Desktop

compcodeR

An R package for benchmarking of differential expression analysis methods, in…

An R package for benchmarking of differential expression analysis methods, in particular methods developed for analyzing RNA-seq data.

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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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cdc_RNASEQ
Desktop

cdc_RNASEQ

A differentially expressed (DE) gene selection algorithm, which controls the…

A differentially expressed (DE) gene selection algorithm, which controls the FDR based on predictive Bayesian estimates. The simulation studies empirically showed that the proposed confident…

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SPARTA
Desktop

SPARTA

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a…

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a bacterial RNA-seq analysis tool performing transcriptional profiling experiments using RNA-seq. It enables microbiologists…

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MetaDiff
Desktop

MetaDiff

A Java/R-based software package that performs differential expression analysis…

A Java/R-based software package that performs differential expression analysis on RNA-Seq based data. By utilizing a meta-regression framework, MetaDiff is able to take advantage of the information…

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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…