Nexus Copy Number - Compare Editions

Nexus Copy Number follows a modular design to optimally meet the user needs and provide the best possible value. The following packaged configurations are designed to be applicable to most user types. However, any configuration can be custom designed and there is never a cost penalty for changing the license configuration.

Nexus Copy Number Discovery Edition - This multi-sample processing configuration is the flagship product designed to provide all the statistical tools needed to conduct copy number based research with maximum ease and speed. It includes all available computational modules as well as Nexus DB.

Nexus Copy Number Standard Edition – This configuration is designed to be a nice complement to Nexus Solo and for those whose work does not require all the analytical functionality in the Disocovery Edition. The Standard Edition allows multi-sample processing, generation of frequency of aberration plots, detection of minimum common regions of gain or loss, and much more. It can also serve as a local database of samples along with sample annotation that can be viewed within the application as well as by Nexus Solo.

Nexus Copy Number Core - This base component can be used to create any custom multi-sample processing and visualization solution meeting the user’s specific needs. Any of the modules listed in the table below can be added to the Core to create a truly custom solution.

Nexus Solo – This configuration is designed to meet the needs of users that need to process and interpret the results of a single sample at a time. This configuration does provide a direct link to Nexus DB so regions of interest can be immediately queried against all samples stored in Nexus DB for which the user has been allowed access. Nexus Solo can display results generated in Nexus Copy Number Standard or Discovery Edition projects.

Reader Clients – All Nexus Copy Number configurations can be licensed as read-only products. This limits the software from processing new samples but all other functions remain fully intact. In fact, with Nexus Copy Number Discovery Edition Reader client you can conduct extensive research by utilizing thousands of already processed samples in Nexus DB without the extra cost of running samples or time spent generating data!

	Solo	Core	Standard	Discovery
Single sample processing, visualization, and interpretation
Allele Specific Computation Module - Allelic event processing and visualization for SNP arrays
Nexus DB - remote storage, backup, retrieval, sharing, and querying	*
Multi-sample processing, visualization, and analysis with sample annotations
Query one or more genes or regions for their genomic alteration status in all samples in a project
Statistical Comparison Module - Identification of regions with statistically significant differences between a pair of sample populations as well as the Predictive Power tool to identify regions that are highly predictive of a continuous valued factor (such as height)
Survival Analysis Module – Includes Survival Predictive Power computation allowing the user to identify regions that are highly predictive of survival with a given statistical significance and allows generation of Kaplan-Meir plots.
External Data Integration Module –Allows for integration of mRNA, miRNA, and methylation analysis results (e.g. Gene lists) to identify genomic hotspot regions. It calculated for each region a p-value indicated the probability of having so many genes in that regions being part of a list by pure chance.
Enrichment Analysis Module – Performs Annotation enrichment analysis identifying pathways and GO terms that are overrepresented in a gene list
Clustering and Factor Enrichment Module – allows the user to group the samples based on genomic aberrations and perform Factor Enrichment
Nexus Expression Module		Optional Add-on	Optional Add-on	Optional Add-on
Nexus Methylation Module		Optional Add-on	Optional Add-on	Optional Add-on

*Nexus Solo does not submit samples to Nexus DB but can query and retrieve from the database