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Gene Expression Data Analysis

Gene Expression Data Analysis

Information Technology supports GeneSpring GX on a high performance workstations. This work station also has other analysis programs installed to meet the needs of analyzing high throughput data (DNA microarray/Affymetrix GeneChip).

This high performance workstation (MS Windows 7 x 64 edition) is located in the GenomeCore Lab (AS8-1030)

To use the designated workstation please contact Phyllis Spatrick, 508-856-4076.

  • GeneSpring Manual

    *See Chapter 2, page 17 for the GeneSpring Quick Tour

    *See Chapter 6, page 139 for analyzing Affymetrix Expression Data

High Performance Workstation Software:

GeneSpring GX version 14.5 

Agilent's GeneSpring provides powerful, accessible statistical tools for intuitive data analysis and visualization. Designed specifically for the needs of biologists, GeneSpring offers an interactive environment that promotes investigation and enables understanding of Transcriptomics, Genomics, Metabolomics, Proteomics and NGS data within a biological context. GeneSpring allows you to quickly and reliably identify targets of interest that are both statistically and biologically meaningful.

  • Multi-omic analysis with Agilent's GeneSpring Bioinformatics Suite
  • Platform for integrated data analysis and biological contextualization
  • Downstream analysis of processed NGS data/ Variant analysis using vcf files
  • Transcriptomic analysis
  • Agilent CGH data visualization and Integration
  • Genomic copy number analysis
  • Genome-wide association analysis
  • Statistical tools for testing differential expression
  • Extensible functionality with Jython and R
  • Report Generation Capability
  • Intuitive graphical displays
  • Built-in ID browser automates database and spectral library searches
  • Support for NGS data visualization


R Package version 3.0.1

R is a software environment for statistical computing and graphics. It compiles and runs on a wide variety of Windows, MacOS and UNIX platforms. R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Alcatel-Lucent) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.