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Gene expression visualization software tools | RNA sequencing data analysis

G T A T C G C T A
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…

G T A T C G C T A
AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

G T A T C G C T A
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…

G T A T C G C T A
Glimma
Desktop

Glimma

Produces interactive graphics. Glimma aims to enable effective interactive…

Produces interactive graphics. Glimma aims to enable effective interactive exploration of data from differential expression (DE) analyses. It returns multi-dimensional scaling (MDS) plot that is an…

G T A T C G C T A
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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QuickRNASeq
Desktop

QuickRNASeq

Advances the automation and visualization of RNA-seq data analyses results.…

Advances the automation and visualization of RNA-seq data analyses results. QuickRNASeq is a pipeline that significantly reduces data analysts’ hands-on time, which results in a substantial…

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htSeqTools
Desktop

htSeqTools

A package with quality assessment, processing and visualization tools for…

A package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. htSeqTools includes detection of outliers and…

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expressionplot
Web

expressionplot

A software package consisting of a default back end, which prepares raw…

A software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse,…

G T A T C G C T A
DeconRNASeq
Desktop

DeconRNASeq

A package for deconvolution of heterogeneous tissues based on mRNA-Seq data.…

A package for deconvolution of heterogeneous tissues based on mRNA-Seq data. DeconRNASeq adopts a globally optimized non-negative decomposition algorithm through quadratic programming for estimating…

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START App
Web
Desktop

START App Shiny Transcriptome Analysis Resource Tool App

Provides researchers with increased flexibility to easily upload and visualize…

Provides researchers with increased flexibility to easily upload and visualize RNAseq data. START App visualizes data in multiple ways that will be useful for scientist to understand their data.…

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RNA-Seq viewer
Mobile

RNA-Seq viewer

Allows users to visualize human genome information as well as the next…

Allows users to visualize human genome information as well as the next generation sequencing (NGS) sequence data information. RNA-Seq viewer is a mobile application available only with iOS…

G T A T C G C T A
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.

G T A T C G C T A
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,…

G T A T C G C T A
oposSOM
Desktop

oposSOM

Bundles a series of sophisticated analysis methods with intuitive visualization…

Bundles a series of sophisticated analysis methods with intuitive visualization options to study high-dimensional data with the special focus on gene-centered expression data. It is designed for a…

G T A T C G C T A
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…

G T A T C G C T A
GEPIA
Web

GEPIA Gene Expression Profiling Interactive Analysis

Enables to perform a diverse range of gene expression analyses. GEPIA is an…

Enables to perform a diverse range of gene expression analyses. GEPIA is an interactive web application which analyzes the RNA sequencing expression data of 9,736 tumors and 8,587 normal samples from…

G T A T C G C T A
TRAPR
Desktop

TRAPR Total RNA-Seq Analysis Package for R

Facilitates the statistical analysis and visualization of RNA-Seq expression…

Facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization,…

G T A T C G C T A
GE-mini
Web
Mobile

GE-mini Gene Explorer

Provides a method for displaying expression profiles of all available tumor and…

Provides a method for displaying expression profiles of all available tumor and tissue types, while allowing drilling down to detailed views for specific tissue types. Users can investigate genes of…

TilingScan
Desktop
Web

TilingScan

A web application for the visualization of strand-specific tiling microarray or…

A web application for the visualization of strand-specific tiling microarray or next-generation sequencing data that allows customized detection of differentially expressed regions all along the…

G T A T C G C T A
BioWardrobe
Desktop
Web

BioWardrobe

Allows users to store, visualize and analyze epigenomics and transcriptomics…

Allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow…

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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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visgenex
Desktop

visgenex

Allows data preparation, analysis and exploration of transcriptome data with…

Allows data preparation, analysis and exploration of transcriptome data with t-SNE (t-statistic Stochastic Neighbor Embedding). Visgenex performs better than commonly used methods, offering insight…

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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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TBro
Desktop

TBro Transcriptome Browser

Aggregates sequences, their annotation, expression levels as well as…

Aggregates sequences, their annotation, expression levels as well as differential testing results. TBro provides an easy-to-use interface to mine the aggregated data and generate publication-ready…

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VOE
Desktop
Mobile
Web

VOE Visual Omics Explorer

A cross-platform data visualization portal that is implemented using only HTML…

A cross-platform data visualization portal that is implemented using only HTML and JavaScript code. VOE is a standalone software that can be loaded offline on the web browser from a local copy of the…

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dictyExpress
Web

dictyExpress

Enables the broad adoption of next generation sequencing (NGS) based inquiries.…

Enables the broad adoption of next generation sequencing (NGS) based inquiries. dictyExpress is a web application designed for exploration of transcriptomics datasets. It allows users to select among…

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VisRseq
Desktop

VisRseq

Provides a visual framework for analysis of sequencing datasets. VisRseq is a…

Provides a visual framework for analysis of sequencing datasets. VisRseq is a computationally rich and accessible framework for integrative and interactive analyses without requiring programming…

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AuPairWise
Desktop

AuPairWise

Measures replicability by modelling the effects of noise within observed…

Measures replicability by modelling the effects of noise within observed co-expression. AuPairWise employs a noise model to perturb a sample in input expression data. It estimates how it affects the…

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Cascade
Web

Cascade

A tool for the visualization of RNA-seq data from cancer genomics projects,…

A tool for the visualization of RNA-seq data from cancer genomics projects, which has the advantages of providing researchers with an intuitive interface for exploring their data in the context of…

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deepTools
Desktop
Web

deepTools

A Galaxy based web server for processing and visualizing deeply sequenced data.…

A Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable…

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ANAQUIN
Desktop

ANAQUIN

Facilitates the analysis of spike-in controls for next generation sequencing…

Facilitates the analysis of spike-in controls for next generation sequencing (NGS). ANAQUIN offers a way for users to evaluate the performance of spike-in controls and the accompanying RNA/DNA…

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VolcanoR
Web

VolcanoR

Allows to analyze the results concerning differential gene expression. VolcanoR…

Allows to analyze the results concerning differential gene expression. VolcanoR takes a table which contains gene name p-value and foldChange as input data. It shows relation between fold change and…

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MiSTIC
Web
Desktop

MiSTIC Minimum Spanning Trees Inferred Clustering

Visualizes and compares collections of gene expression profiles, instantly…

Visualizes and compares collections of gene expression profiles, instantly highlighting differences and similarities in gene clustering between cancer types or subtypes. MiSTIC should facilitate…

G T A T C G C T A
SwitchSeq
Desktop

SwitchSeq

A tool to identify, annotate and visualise splicing switch events from RNA-seq…

A tool to identify, annotate and visualise splicing switch events from RNA-seq data. By relying on transcript level quantifications, SwitchSeq provides a simple (yet powerful) approach to identify,…

MeV
Desktop
Web

MeV Multiple experiment Viewer

Allows to analyse, visualise and stratify large genomic data. MeV is a…

Allows to analyse, visualise and stratify large genomic data. MeV is a cloud-based application that gives access to genomic analysis tools, large public domain data sets, intuitive user interfaces,…

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HTSFilter
Desktop

HTSFilter

Calculates a filtering threshold for replicated RNA sequencing data. HTSFilter…

Calculates a filtering threshold for replicated RNA sequencing data. HTSFilter provides an intuitive data-driven way to filter RNA-seq data and to effectively remove genes with low constant…

G T A T C G C T A
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…

G T A T C G C T A
MicroScope
Web
Desktop

MicroScope

A ChIP-seq and RNA-seq software suite for visualizing and analyzing genomic…

A ChIP-seq and RNA-seq software suite for visualizing and analyzing genomic data, including features to support differential expression analysis, heatmap production, principal component, gene…

G T A T C G C T A
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…

G T A T C G C T A
CummeRbund
Desktop

CummeRbund

A tool for visualizing RNA-seq analysis results. CummeRbund takes the various…

A tool for visualizing RNA-seq analysis results. CummeRbund takes the various output files from a cuffdiff run and creates a SQLite database of the results describing appropriate relationships…

TreeView
Desktop

TreeView

Allows visualization of microarray data. TreeView is an open source,…

Allows visualization of microarray data. TreeView is an open source, cross-platform which offers several views, including dendrogram, scatterplot, karyoscope and alignment, with visual cues to show…

G T A T C G C T A
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…

G T A T C G C T A
tbrowse
Web

tbrowse

This project aims to provide a simple, intuitive browser for exploring RNA-seq…

This project aims to provide a simple, intuitive browser for exploring RNA-seq data in the familiar track layout of common genome browser.

G T A T C G C T A
debrowser
Web
Desktop

debrowser

Allows users to visualize expression data. debrowser is customizable by user,…

Allows users to visualize expression data. debrowser is customizable by user, this permits to consult different parts of the contents. This tool assists users to do plots easily without writing any…

G T A T C G C T A
ViennaNGS
Desktop

ViennaNGS

An integrated collection of Perl modules focused on building efficient…

An integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. ViennaNGS comes with functionality for extracting and converting features from common NGS…

G T A T C G C T A
dSpliceType
Desktop

dSpliceType

A generalized framework to systematically investigate the synergistic and…

A generalized framework to systematically investigate the synergistic and antagonistic effects of differential splicing and differential expression. dSpliceType detects and prioritizes a list of…

G T A T C G C T A
sRAP
Desktop

sRAP

Provides a pipeline for gene expression analysis (primarily for RNA-Seq data).…

Provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions of sRAP (Quality Control Figures,…

G T A T C G C T A
iCanPlot
Desktop
Web

iCanPlot Interactive HTML5 Canvas Plotting Library

A compelling platform for visual data exploration based on the latest…

A compelling platform for visual data exploration based on the latest technologies. iCanPlot is a highly interactive tool to visualize tabular data and identify interesting patterns in an intuitive…

G T A T C G C T A
ShinyNGS
Desktop

ShinyNGS

Facilitates downstream analysis of RNA-seq and similar expression data.…

Facilitates downstream analysis of RNA-seq and similar expression data. ShinyNGS provides Shiny applications for various array and Next-Generation Sequencing (NGS) applications. The software allows…

G T A T C G C T A
rnaseqview
Desktop

rnaseqview

Enables users to visualize genome-wide expression data from NCBI's…

Enables users to visualize genome-wide expression data from NCBI's Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. rnaseqview extracts aligned RNA-Seq data from SRA or…

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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,…

Qlucore Omics…
Desktop

Qlucore Omics Explorer

Provides bioinformatics products to support the user with visual analysis of…

Provides bioinformatics products to support the user with visual analysis of measured data taking into account publicly available information such as gene ontologies, pathways and other system…

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Degust
Web

Degust

A web tool to help you analyse, visualize and fully appreciate your…

A web tool to help you analyse, visualize and fully appreciate your differential gene expression data from RNA-seq experiments. Degust consists of a backend that uses limma and edgeR to perform the…

G T A T C G C T A
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.

G T A T C G C T A
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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ExProView
Web

ExProView

Allows efficient analysis of large data sets from mRNA expression studies…

Allows efficient analysis of large data sets from mRNA expression studies obtained from expressed sequence tag (EST) sequencing. ExProView offers different types of data access and visualization. It…

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