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Resources and Software

iPathwayGuide

iPathwayGuide enables IIHG Bioinformatics to analyze gene sets from RNA-Seq, ChIP-seq, ATAC-seq, microarrays, or other gene or protein expression experiments to identify the pathways, biological processes, networks, molecular functions, diseases, and cellular components that are implicated in a given phenotype.  In addition, iPathwayGuide provides sophisticated meta-analysis capabilities, as well as the ability to identify active microRNAs from mRNA data.  We create a cloud-based report from your gene set and share that report with you.  There is no software to install and no limit on the number of end-users or sharing of reports!  

Galaxy

The IIHG also has a local instance of Galaxy, a very friendly way to access high throughput bioinformatics tools through a web browser interface. If you have a hawkid, you can simply click here and set up an account. Please note, the Galaxy install is free to use and does not limit storage resources like the main instance of Galaxy. However, if you have more than 500Gb of storage for more than three months, we will begin to bill for storage according to our fee schedule.

GenomeTrax®

The IIHG also has access to GenomeTrax®, a highly-specialized database useful for annotating human variants. Due to licensing terms, it is only currently available to members of the Iowa Institute of Human Genetics. It is in the form of a Mysql database which is very useful for high throughput programmatic access but it does not have a friendly user interface. This software is primarily for advanced users.


Legacy support for: 

Ingenuity Pathway Analysis®

Ingenuity Pathway Analysis® (IPA).  IPA may be used for several applications, including transcriptomics, microRNA analysis, target discovery, drug repositioning, proteomics and metabolomics. To learn more about the University of Iowa's IPA license and how to get access click here.   

(Please note: IIHG Bioinformatics continues to provide access to IPA for the near term for legacy users, but it is no longer our recommended or preferred pathway analysis tool.  We strongly suggest you inquire with us about iPathwayGuide reports for your next project!)

Partek Genome Studio®

Partek Genome Studio offers point and click analysis for microarray and limited next generation analysis.  Please contact iihg-bioinformatics@uiowa.edu for more information.  (It is not possible to use Partek GS for RNA-seq analysis if you have raw sequencing reads.  Please consider using Galaxy or contacting us for help).