Nexus Copy Number™

Offering simple yet powerful tools for CNV analysis and visualization from aCGH, SNP array and NGS data.


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Nexus Copy Number is a multifaceted desktop software for rapid discovery of genomic alterations. The interactive visualization and powerful statistical tools allow detection of structural variations (e.g. copy number, homozygous regions), association with sequence variations (point mutations, InDels, inversions, etc.), and identification of statistically significant co-occurring up/down regulated genes (from mRNA, miRNA, and RNASeq data).

The new version allows users without bioinformatics expertise, to easily import BAM files to visualize/analyze copy number as well as LOH and allelic Imbalance events. Learn more.

Cancer specific analysis

Nexus Copy Number supports many different types of samples but some such as cancer samples require specialized tools. Cancer-specific algorithms in the software provide for ploidy of samples, percent tumor burden, and detection of low-level mosaic events. Additional features include survival analysis (including Kaplan-Meier plots), gene enrichment analysis, and identification of statistically significant coordinating events. Nexus Copy Number also provides easy access to high fidelity, manually curated data from TCGA (The Cancer Genome Atlas) via the TCGA Premier product.


Copy number from NGS


The latest release, Nexus Copy Number version 8.0, offers copy number estimation from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing panels. The sophisticated algorithm in Nexus Copy Number requires only BAM files as input and in addition to copy number, also derives B-allele frequencies (BAF) from BAM files.

Integrated gene expression results

Nexus Copy Number is a truly integrated product allowing joint analysis between different data modalities. With version 8.0, gene expression results (from mRNA, miRNA, and RNASeq) can be incorporated on a per sample basis allowing identification of genes highly correlated between the two data modalities.

Go from Raw Data to Advanced Analysis in Minutes!

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System Requirements:
32-bit Platforms Supported: Windows Win2k/WinXP/Win7 • Minimum: 1.0 GHz Pentium, 1 GB RAM • Recommended: 2.0 GHz or faster, 2 GB RAM
64-bit Platforms Supported: Windows/OSX/Linux • Minimum: 2 GB RAM • Recommended: 4 GB RAM

Nexus Copy Number Features

Enrichment Analysis

Performs annotation enrichment analysis identifying pathways and GO terms that are overrepresented in a gene list.

Sequence Variant Analysis

Analysis and visualization of sequence variants (point mutations, InDels, inversions, etc.) from VCF and MAF files, concurrently with copy number and allelic events.

Clustering and Factor Enrichment

Clustering groups samples based on genomic aberrations and factor enrichment identifies those factor values with a statistically significant over-representation in a specified phenotype/factor under study.

Survival Analysis

Performs Survival Predictive Power computation allowing identification of regions that are highly predictive of survival with a given statistical significance and allows generation of Kaplan-Meir plots.

 Single sample gene expression integration

Helps identify genes highly correlated between copy number/allelic event aberrations and gene regulation states.

Statistical Comparison

Allows comparison of two groups of profiles and identifies statistically significant differences in genomic changes between the two groups.

External Data Integration

Allows for integration of mRNA and miRNA results (e.g. Gene lists) to identify genomic hotspot regions. It calculates for each region a p-value indicating the probability of having so many genes in that region as part of a list by pure chance.

Predictive Power

Makes correlations between genomic alterations and continuous value factors (e.g. age at diagnosis)


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Copy number and allele-specific computation

Generates copy number events from different technologies (aCGH, SNP array, NGS) and LOH and allelic events from SNP arrays and NGS (whole-exome, whole-genome, targeted panels).

External Data Integration

Allows for integration of mRNA and miRNA results (e.g. Gene lists) to identify genomic hotspot regions. It calculates for each region a p-value indicating the probability of having so many genes in that region as part of a list by pure chance.

Nexus DB

A secure, genomic data repository for project backup and sharing among collaborators and with access to select public data from databases such as GEO and TCGA.


Allows identification of cooperating events (e.g. what copy number alterations are associated with ERBB2 gain in my sample set?)


Nexus Copy Number Array

For analysis of aCGH and SNP arrays from vendors like Affymetrix Agilent, OGT, and Illumina.

Nexus Copy Number NGS

For analysis of NGS data (WES, WGS, targeted panels) supporting .BAM and .VCF files.

Nexus Copy Number Discovery

For analysis of array (aCGH and SNP) and NGS (WES, WGS, targeted panels) supporting .BAM and .VCF files.

BioDiscovery Benefits


Able to handle and process data from all commercial platforms.


Optimum usage of computing.

Acute Sense of Fitness for Purpose

Usefulness to our community of users.

These products empower Biologists and Geneticists with sophisticated, yet highly usable tools to analyze and interpret their data and draw meaningful conclusions.