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Partek Genomics Suite (PGS): Overview

Main Applications

Partek Genomic Suite (PGS) is a comprehensive suite for statistical analysis and visualization of both microarray and Next-Generation Sequencing data.

Microarray Data Analysis
(all major platforms such as Affymetrix, Illumina, etc.)
Complete workflow from raw data to significant gene list

  • Gene and exon expression
  • Regulation data (ChIP-on-chip, methylation, promoter tiling arrays)
  • microRNA expression
  • SNP and copy number analysis
  • Genome-wide association analysis

Next-Generation Sequencing Data Analysis
(all major platforms such as Illumina, SOLiD, Ion Torrent, etc.)
Statistical workflow from aligned reads (BAM files) to significant gene list

  • RNA-seq
  • DNA-seq
  • ChIP-seq
  • microRNA-seq
  • methylation-seq


  • Heatmap
  • PCA plots
  • Hierarchical and partitioning clustering
  • Survival curves
  • Time-serie profile trellis

Why use PGS?

PGS is one of the most widely-used and high-performance tools for genomic data analysis

  • Easy to follow user friendly workflows
  • Powerful statistics and interactive visualization
  • Direct import of raw/processed microarray data and aligned sequencing reads (BAM files)
  • Quick identification of significantly altered genes

Access PGS @ USC

USC has licensed PGS for the free use of USC faculty, students and staff. The license consists of TWO concurrent user seats.  There are three ways you can access PGS:

  1. On your own computer
    (requires local installation of PGS)

    Requires USC fixed IP addresses -computers connected to USC network via Ethernet cable
  2. On NML-Bioinfo workstations computers
    (no installation needed)
    Available in the Norris Medical Library's Bioinformatics Computation and Consulting Center (top floor)
  3. On HPCC-NML
    (no installation needed)
    Requires HPCC account AND access to the HPCC-NML Bioinformatics Computing Resource.  Account processing may take 1-3 weeks.

To get your PGS account:

  1. Carefully check out the PGS user policy
  2. Fill out the PGS registration form

Need help?

Get started

  • Task-oriented tutorials (PDF documents):
    these are great resources to get you started

Help @ Partek Inc.

  • Partek support is very approachable.  The support team can initiate teleconference and show you the procedures interactively on your screen
  • Contact Partek support
  • Webinars: check schedules

Help @ NML Bioinformatics