Biodiscovery Nexus Software

BioDiscovery Nexus Software
Nexus Copy Number – Accelerating Copy Number Analysis Research

Nexus Copy Number™ software offers simple yet powerful tools for copy number (CNV) and sequence variation analysis and visualization from aCGH, SNP array as well as next-gen sequencing (NGS) data. The framework can be used for projects as small as a few samples and scales to tens-of-thousands of samples in a single study.

The user-interface and powerful statistical tools are designed specifically for the end-user allow detection of structural variations (copy number, homozygous regions – sometimes called LOH, AOH, or LCSH), association with sequence variations (point mutations, InDels, inversions, etc. from VCF, MAF, or text files), and identification of affected pathways.

Population-wide discovery tools include gene enrichment, survival analysis (Kaplan-Meier, predictive power), between-group comparisons, concordance for finding multi-hit events, GISTIC, STAC, and a host of user-friendly displays for dynamic interaction with your data. Single-sample processing includes algorithms optimized for heterogeneous cancer samples (e.g., SNP-FASST2 segmentation with user-defined parameters, matched-normal processing, ASCAT) and recent additions for imputing copy number from NGS platforms.

Recent posts on the utility of the software from BioDiscovery can be found here:

Educational and training videos can be found here: and webinars can be found here:

TCGA Premier is included in CCR’s license agreement:  Curated CNVs, Sequence Variants, Simplified Access

The Cancer Genome Atlas (TCGA) is an amazing resource, growing to contain genomic profiles of approaching 12,000 tumors across more than thirty cancer types. The TCGA project has already proven useful in large-scale studies; however, these early studies have principally found the “low hanging fruits”, and the voluminous data generated by this project has great additional potential.

By re-analyzing the data and manually curating the results of each sample by trained scientists, the TCGA Premier database has the highest fidelity copy number information from this rich resource.  TCGA Premier is already integrated with Nexus Copy Number software, allowing users to quickly query the database, retrieve samples of interest along with annotations, and perform further analysis all through the Nexus interface.

Improved Copy Number Profiles
Each sample is re-processed from the “raw” (i.e., level 1) data, then manually reviewed by a team of scientists ensuring the highest fidelity CNV calls.

Integrated Sequence Variants
Sequence variants obtained by whole-exome sequencing are integrated with CNVs, providing a more comprehensive genomic picture.

Nexus Interface to the TCGA
Query by gene, region, an event, or clinical annotation – typically in seconds. Data can be downloaded to your Nexus project and integrated with other data sources for more robust analyses

Nexus Expression – A new take on microarray gene expression analysis

Nexus Expression is a solution that is computationally very powerful but simple to use by scientists for answering common research questions. Our design objectives for this package have been the same as our very successful Nexus Copy Number product:

  • A platform independent solution (support for all commercial platforms and custom arrays)
  • Efficient processing on a basic desktop computer (hundreds of high-density arrays can be processed in one project)
  • A user-friendly interface designed for end-user researchers, not informaticians (no programming knowledge needed)

Nexus Expression provides an intuitive and streamlined approach to convert raw signal values into meaningful information by integrating sample phenotypes (e.g., disease stage, survival, age, sex, etc.) with gene annotations (e.g. GO terms). Users can effortlessly navigate large datasets and generate results with a few mouse clicks. For example, in a cancer study, differentially regulated genes in the HER2 positive sub-population as compared to HER2 negative can be identified in one click and the affected biological processes can be identified with another click. Using a sophisticated ANOVA engine under the hood, the user can easily compare between subgroups, cluster samples, and genes, view annotations and perform gene enrichment all with single clicks. Nexus Expression is platform agnostic so data from multiple commercial and custom platforms can be loaded, processed, and viewed with ease.

Access Information

To get Nexus installed on your lab computer, please submit a request through “NCI at Your Service” to obtain access to Nexus Software.