Gene expression visualization software tools | RNA sequencing data analysis

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 betweeen genes, transcripts, transcription start sites, and CDS regions. Once stored and indexed, data for these features, even across multiple samples or conditions, can be retrieved very efficiently and allows the user to explore subfeatures of individual genes, or genesets as the analysis requires.

Enables users to perform a diverse range of gene expression analyses. GEPIA is an interactive web application that analyzes the RNA sequencing expression data of more than 9,000 tumors and 8,000 normal samples from The Cancer Genome Atlas (TCGA) and the GTEx projects. It provides customizable functions such as tumor/normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis.

Allows users to handle RNA-sequencing pipeline based on the TopHat, Cufflinks and CummeRbund suite of software. Tuxedo is a program that enables assessment of alternative splicing (AS) inferred on fragments per kilobase per million (FPKM) values. It can assist researchers to detect genes and splicing variants and compare gene expression and transcripts under different conditions.

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, data visualization, and tools for reproducible research. The software allows user to explore the large public data sets, develop and test hypotheses and extend those explorations to their own data. It was designed for use in a variety of different scenarios.

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 users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner.