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.
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.
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 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.
Enables interactive query and navigation of transcriptome datasets relevant to human immunology research. GXB can be used to browse context-rich systems-scale data within and across systems immunology studies. It can handle the large collections of datasets generated through systems-scale profiling approaches. The tool can be used to display other data types, such as protein or cellular measurements, regardless of whether they are high dimensional.
Enables the discovery of potential subtypes of known diseases. PhenoX is a proof of principle tool that performs disease subtyping using publicly available gene expression data and literature. The software aggregates and clusters gene expression data to determine potential disease subtypes, and develops a phenotypic profile for each subtype using term co-occurrences in published literature. It is also amenable to future expansions of Gene Expression Omnibus (GEO) expression cataloging.