GenomeSpace Tools and Data Sources

GenomeSpace hosts a variety of tools and data sources that provide a wide spectrum of genomic analysis and bioinformatics capabilities. If you would like to add your tool to the GenomeSpace community, see our developer information or contact us.

Tool Description

Cytoscape

 Cytoscape is an open-source bioinformatics software platform for visualizing molecular interaction networks and biological pathways, and integrating these networks with annotations, gene expression profiles, and other state data.   Cytoscape core distribution provides a basic set of features for data integration and visualization.  Additional features are available as plugins.  Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.  Plugins may be developed by anyone using the Cytoscape open API based on Java™ technology and plugin community development is encouraged. Most of the plugins are freely available.

Galaxy

 The Galaxy project is an open, web-based platform for performing accessible, reproducible, and transparent biomedical research. Complete computational analyses can be built, saved, rerun, modified, and shared. Galaxy is available as a free public web server; as open-source software that can be installed and customized to address specific needs; as a virtual machine that can be installed on the cloud; and on many specialized public web servers at user sites.

GenePattern

 GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

Genomica

 Genomica is an analysis and visualization tool for genomic data, which can integrate gene expression data, DNA sequence data, and gene and experiment annotation information. Using Genomica, you can do the following:

IGV

 The Integrative Genomics Viewer (IGV) is a light-weight, high-performance visualization tool that enables intuitive real-time exploration of diverse, large-scale genomic data sets on standard desktop computers. It supports flexible integration of a wide variety of data types including aligned sequence reads, mutations, copy number, RNA interference screens, gene expression, methylation, and genomic annotations. IGV makes use of efficient, multi-resolution file formats to enable real-time exploration of arbitrarily large data sets over all resolution scales, while consuming minimal resources on the client computer.  Navigation through a data set is similar to that of Google Maps, allowing the user to zoom and pan seamlessly across the genome at any level of detail from whole genome to base pair.

UCSC Table Browser

 The UCSC Genome Browser website contains the reference sequence and working draft assemblies for a large collection of genomes. The Table Browser provides convenient access to the underlying database, allowing you to retrieve the data associated with an annotation track (a means of organizing a particular set of information, such as known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, or chromosomal bands) in text format, to calculate intersections between tracks, and to retrieve DNA sequence covered by a track.

InSilico DB

 InSilico DB is a Web application that provides a powerful and intuitive interface to a large repository of gene expression datasets, including the contents of Gene Expression Omnibus (GEO).

Cistrome

 A cistrome is defined as the set of cis-acting targets of a trans-acting factor on a genome scale. The Cistrome project integrates ChIP-chip/seq data for a cistrome with standard analysis pipelines, while  providing users with a user-friendly, powerful, flexible web interface with which they can access the data and pipelines.

In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses, to downstream genome feature association, gene expression analyses, and motif discovery.

geWorkbench

 geWorkbench (genomics Workbench) is an open source Java desktop application that provides access to an integrated suite of tools for the analysis and visualization of data from a wide range of genomics domains (gene expression, sequence, protein structure, and systems biology). More than 70 distinct plug-in modules are currently available, implementing both classical analyses (several variants of clustering, classification, homology detection, etc.) as well as state-of-the-art algorithms for the reverse engineering of regulatory networks and for protein structure prediction, among many others. geWorkbench leverages standards-based middleware technologies to provide seamless access to remote data, annotation, and computational servers, thus enabling researchers with limited local resources to benefit from available public infrastructure.

ArrayExpress

 The ArrayExpress Archive is a database of functional genomics data; it stores microarray and high-throughput sequencing (HTS) data that are described and archived according to the community guidelines for microarray (MIAME) and HTS (MINSEQE) data.

Gitools

 Gitools is a framework for analysis and visualization of genomic data using interactive heatmaps that also allows data to be imported from various sources, including Biomart, Ensembl, IntOGen, and GenomeSpace.

ISAcreator

 The open source ISA metadata tracking tools help to manage an increasingly diverse set of life science, environmental, and biomedical experiments that employ one or a combination of technologies.

MSigDB Online Tools

 The Molecular Signatures Database (MSigDB) is a large curated collection of annotated gene sets.  It has some accompanying online tools, including one that allows you to compute the overlap between your own gene set and the MSigDB gene sets.  When gene sets share genes, examination of how they overlap can highlight common processes, pathways, and underlying biological themes. This tool evaluates the overlap of a user-provided gene set, and an estimate of the statistical significance, with as many MSigDB collections as you choose.