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Partek Genomics Suite

Description

Partek Genomics Suite (Partek) is a graphical user interface (GUI) based bioinformatics package. It hosts a range of work flows that allow for gene expression, epigenetic, and association analysis.

Listing of Analysis Functions

Genome wide association and inheritance

  • Analysis using data derived from arrays
  • Association
  • Trio
  • Analysis using data derived from sequencing
  • Trio

Genetic variants

  • Analysis using data derived from arrays
  • Copy number
  • Allele specific copy number
  • Loss of heterozygosity
  • Analysis using data derived from sequencing
  • Find single nucleotide variants
  • Annotate single nucleotide variants
  • Predict single nucleotide variants effects

Gene expression

  • Microarray
  • Human exon array
  • RNA sequencing

Gene regulation

  • Promoter tiling array

Epigenetics

  • Methylation array
  • ChIP sequencing
  • Bisulfite sequencing

Biological insigts

  • Pathway analysis and gene ontology

Phenotypic outcome

  • Survival analysis

Visualizations

  • Genome browser

Information mining

  • Import NCBI GEO data

Recommendations

Note that Partek Genomics Suite does not handle NGS read mapping but will accept mapped data in the form of BAM files. This package does not offer functionalities for basic molecular biology analysis such as sequencing alignment, phylogenetics, or primer design. For these, the user should look to CLC Genomics Workbench, Geneious Prime, Snapgene, or Lasergene. If the user needs to conduct trio analysis, Partek Genomics Suite is an option to turn to (another package that handels trio analysis is CLC Genomics Workbench).

Things to Know

Partek Genomics Suite is made by the company that develops Partek Flow and serves a good option for users to conduct analysis outside of Biowulf. A reason for using Partek Genomics Suite is for trio analysis, which is a feature that Partek Flow does not have.

Input Data Types

  • CSV
  • TXT
  • CEL
  • CHP
  • CNCHP
  • CNVCHP
  • MIP
  • ARR
  • GPR
  • IDAT
  • SAM
  • BAM
  • VCF
  • BCF
  • Partek Genomics Suite also allows for import of data obtained from the following platforms
  • Fluidigm
  • Nanostring
  • NimbleGen

Output Data Types

  • TXT
  • TSV
  • CSV
  • HTML
  • PNG
  • SVG
  • PDF
  • PPM
  • JPEG
  • GIF
  • PS

Access Information

You must submit a request through service.cancer.gov to obtain access to Partek Genomics Suite. This software requires access to a floating license server, and so care should be taken to return licenses when the software is not actively being used (i.e. close the application). Connection to NIH network or VPN is necessary to use Partek Genomics Suite. OSTR has 10 licenses to this package.

Getting Help

To access the Partek Genomics Suite documentation, click here.