Topic: Nexus Tips Tricks

How does clustering work in Nexus Copy Number?

When studying genomic data, we are often looking for similarities and differences among a group of samples. We try to see if there are any patterns and whether the samples group together into subsets based on gain and loss profiles. One way to do this is with a clustering function. clustering.pngIn Nexus Copy Number, clustering is done by clicking on the "Cluster" button on the "Results" tab.

For CNV analysis, how do I combine data from different sources into a single Nexus Copy Number project?

You already know that Nexus Copy Number is a versatile software for genomic data analysis that can load and process data from different technologies (arrays, NGS), manufacturers (Agilent, Affymetrix, Illumina…), and modalities (copy number, sequence variants, gene expression, methylation).

Linked Sample Analysis in NxClinical 2

Looking to do some analysis where you need to take into account a relationship between samples? Even though NxClinical 2.2 performs analysis only on a single sample level, you can create links between samples and view these together.

Estimating Copy Number From Log Ratios

Take a look at some common questions that customers have about using Nexus, and receive some advice on calculating the actual copy number of samples in Nexus.

Genome Annotations – Now on the Downloads page!

You can now easily add new organisms to your genome annotation files, like cows, dogs, or cats. Download the annotation files and get started today.

Converting copy number to values in Excel

Looking to convert descriptive results from copy number like “homozygous copy loss”, and “High Copy Gain” to excel? This formula helps keep it simple.

Notes on Analyzing Affymetrix OncoScan™ Data in Nexus Copy Number

Learn why Nexus Copy Number is the exclusive software solution for the analysis of OncoScan™ data due to its advanced algorithm and ease of use.

Concordance: Identifying Significant Co-occurring Alterations

After identifying a copy number change or a sequence variant, you may wonder, what other changes are associated with this aberration? Find out here!

Changing Analysis Settings in Nexus

The default Nexus Copy Number settings is great, but if you want to learn how to adjust the settings to optimize results, we've got you covered!

RNASeq for Differential Gene Expression

Learn how to estimate the number of mRNA transcripts for differential gene expression between sample phenotypes. using RNASeq protocol.