Tools

g2nb hosts a variety of tools and data sources that provide a wide spectrum of genomic analysis and bioinformatics capabilities.

Tool Description How to access in g2nb
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. Tool Panel
GenePattern GenePattern is a powerful genomic analysis platform that provides access to hundreds of 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. Tool Panel
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. Tool Panel
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. Tool Panel
NDEx The NDEx Project provides an open-source framework where scientists and organizations can share, store, manipulate, and publish biological network knowledge. Github import ndex2
Globus Connect With Globus, subscribers can move, share, and discover data via a single interface – whether your files live on a supercomputer, lab cluster, tape archive, public cloud or your laptop, you can manage this data from anywhere, using your existing identities, via just a web browser. Documentation Globus Panel
FireCloud A scalable cloud-based platform for collaborative genome analysis Documentation import firecloud