Nexus Copy Number - Frequently Asked Questions
I want to use one software package to analyze my data from several different array platforms. Does Nexus allow me to do this?
Nexus Copy Number supports data generated by any platform or technology. The software offers direct loading and processing of data from Affymetrix (CEL, CNCHP, CNAT), Agilent FE (TXT), Illumina (GenomeStudio Plug-In), Roche NimbleGen (NimbleScan TXT), ImaGene (TXT), GenePix (GPR), and many more formats. A Nexus project can combine data from arrays of different density as well as different manufacturers.
Data interpretation is taking too long. How can Nexus speed up the process without compromising the accuracy of my results?
Nexus Copy Number was designed from the ground up to facilitate an efficient review of samples while integrating data from various public and local databases. The software provides information at multiple levels of detail allowing the user to start from the genome, zoom-in on a detected aberration, review genomic annotations for the area (e.g. genes, miRNA, exons, known CNVs etc.), query for other samples with similar aberrations, review probe level data, etc. A simple workflow is outlined in Simplifying Data Interpretation with Nexus Copy Number.
How can Nexus dramatically increase my productivity to get the most out of my data quickly and accurately?
With Nexus Copy Number you can load and process data associated with a project having hundreds of samples in a couple of hours and integrate phenotype data to all samples with a single click. At that point you are ready to answer your biological questions with just a single click. For example:
- What are the regions of minimum common aberration that are present in at least 25% of my samples (one-click)? How many and what are the genes in these regions (one-click)? What are the biological processes that are being affected most by these genes (one-click)?
- What are the areas of significant difference between case and control populations (one-click)?
- What are the areas that are highly predictive of survival outcome (one-click)?
- And much more
Can I quickly compare my results with published data and easily share results with my collaborators across the globe?
Nexus Copy Number version 5 integrates with Nexus DB, a cloud based repository. Nexus DB holds data that has been processed via Nexus client software and the "public" area contains results from publically available sources, such as The Cancer Genome Atlas (TCGA) data, HapMap data, and many individual publications. This data can be used to increase the statistical power of your analysis or can be used as validation for findings based on your data.
In addition to accessibility to public data, users have complete control over access rights to their data and can participate in various global collaborations providing access to their data to only a select group of collaborators.
I am doing very large scale analysis with thousands of samples that were run on very high density arrays. Can Nexus handle this?
Nexus Copy Number can create and manage projects with many thousands of very high-density samples without requiring more than an average desktop computer CPU speed or memory. It also provides the FASST algorithm for efficiently and accurately processing very high density (>2M probes) arrays.
What organisms does Nexus support?
Nexus Copy Number can work with any organism genome. It is installed with genomes for Human, Mouse, Monkey, Dog, ...but any model organism can be analyzed.
Can Nexus easily integrate expression, miRNA and/or methylation analysis results with copy number data?
Results of gene, miRNA, and methylation experiments either generated using a software program like Nexus Expression or obtained from other applications can effortlessly be imported into Nexus Copy Number and visualized. Statistical algorithms are used to identify hot-spots where there is a high degree of overlap with changes in copy number and reported changes in other modalities.
