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Ingenuity Pathway Analysis (IPA)

Ingenuity Pathway Analysis (IPA) is a web-based software application for the analysis, integration, and interpretation of data derived from -omics experiments, such as RNAseq, small RNAseq, microarrays including miRNA and SNP, metabolomics, proteomics, and small scale experiments that generate gene and chemical lists. Powerful analysis and search tools uncover the significance of data and identify new targets or candidate biomarkers within the context of biological systems. For more information, visit http://www.ingenuity.com/products/ipa.

IPA access is available on a for-fee basis through a single workstation located in the BioConnector area in the Health Sciences Library. See the following links for how to create an account, reserve your computing time via iLab, and view fees for use.

Software Access

Note for first time users: you will need to change the IPA settings to maximize performance.

  • In IPA, go to File ->Preferences ->Application Preferences
  • Choose System memory allocated to IPA – choose 3000mb or 4000mb
  • Go to Cache tab and set at 2000 

Ways to Get Help

1. Free Basic Support

Contact support@ingenuity.com

Customer Support at IPA: http://www.ingenuity.com/customer-support

Online Training and Videos: 

iLab Support is available at: support@ilabsolutions.com

2. For-fee Support for IPA from the SOM Core Facilities

Assisted use for IPA is available for a fee with Brian Capaldo, a data analyst in the School of Medicine Core Facilities. Assisted use must be scheduled in advance through the ORCA Admin Core on iLab. For urgent issues regarding IPA, users should consult the IPA tutorials or contact IPA customer support. Assistance in preparing data for use in IPA or interpreting results is also available. Consult the IPA assistance calendar in iLab to view rates and schedule assisted IPA use, data preparation, or results interpretation. 

For more information, contact Brian Capaldo at bc2zb@virginia.edu.

3. For-fee support for Current and Follow-on -Omics Studies from Bioinformatics Core

Support for current and follow-on -omics studies:

  • Study design (sample size & sequencing configuration)
  • Data analysis (e.g., alignment, quantitation, finding candidate genes of interest, etc.)
  • Custom / study-specific data management, manipulation, & visualization
  • Help interpreting -omic data in a biological context
  • Grant support & manuscript preparation

The above support is offered for a wide range of -omics data, including but not limited to:

  • RNA-seq or microarray
  • Single-cell RNA-seq
  • ChIP-seq
  • Other *-seq (ATAC-seq, PAR-CLIP, DNAse-seq, MEDIP-seq, etc)
  • Methylation analysis
  • Whole genome/exome

For more information contact bioinformatics@virginia.edu.

4. Data Transfer  

Data can be imported into IPA via any means available to public UVa computers such as a portable hard drive or attachments.

  • IPA doesn’t take raw data – Text, Excel, cuffdiff files types only.  Need help?  Contact bioinformatics@virginia.edu
  • Data should not be stored locally: any and all users would have access to it
  • Users who leave data on the computer may have to schedule a new reservation at the full rate to remove data

To schedule a personalized training session or for any questions, contact bioconnector@virginia.edu.  We will try to connect you with the right person.