Allows users to compare two or more groups of Samples in a GEO Series in order to identify genes that are differentially expressed across experimental conditions. GEO2R performs comparisons on original submitter-supplied processed data tables using the GEOquery and limma R packages from the Bioconductor project. This tool provides a simple interface that allows users to perform R statistical analysis without command line expertise. Results are presented as a table of genes ordered by significance.
A package that allows access to the wealth of information within GEO directly from BioConductor, eliminating many formatting and parsing problems that have made such analyses labor-intensive in the past. The primary goal of GEOquery is to download and parse the SOFT format files from GEO, maintaining all of the information contained in the GEO records. The design of GEOquery makes accessing data from GEO very simple. There is only one command that is needed, getGEO. GEOquery provides a bridge between the BioConductor analysis tools and the vast public data resources contained in the NCBI GEO repositories. By maintaining the full richness of the GEO data rather than focusing on getting only the ‘numbers’, it is possible to integrate GEO data into Bioconductor data structures and to perform analyses on that data quite quickly and easily or to export the data into any number of formats for use by other tools or for local storage and data mining.
Offers access to over 180 tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. GenePattern is a genomic analysis platform that provides tools in the form of modules. Users can submit their data and choose suitable settings for performing complex analyses without detailed knowledge of the underlying programming language, algorithms and settings.
An innovative online platform to help you interpret your results, prioritize targets and biomarkers, identify correlated genes, discover novel disease-specific genes, or simply to explore the world's gene expression data. The search engine processes measurement data from 17 organisms.
A web-based tool that can query a database comprising ∼4300 microarrays, representing human gene expression in normal tissues, cancer cell lines and primary tumors. MERAV has been designed as a powerful tool for whole genome analysis which offers multiple advantages: one can search many genes in parallel; compare gene expression among different tissue types as well as between normal and cancer cells; download raw data; and generate heatmaps; and finally, use its internal statistical tool. Most importantly, MERAV has been designed as a unique tool for analyzing metabolic processes as it includes matrixes specifically focused on metabolic genes and is linked to the Kyoto Encyclopedia of Genes and Genomes pathway search.
Enables re-processing and re-analysis of Gene Expression Omnibus (GEO) RNA-seq data. GREIN is a web application composed of a back-end computational pipeline (GREP2) for uniform processing of RNA-seq data and several already processed data sets. The software offers features such as sub-setting and downloading of processed data, interactive visualization, statistical power analyses, construction of differential gene expression signatures and their comprehensive functional characterization, or connectivity analysis with LINCS L1000 data.
Identifies genes showing similar expression or response profiles from selected databases. Expression Angler employs the Pearson correlation coefficient to identify co-regulated genes. It provides powerful means to query the data. This tool can recognize marker genes for genotoxic stress and different kinds of pathogen response. It uses the pattern to search for genes with similar expression profiles.