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Ingenuity Pathway Analysis plugin latest improvements

Ingenuity Pathway Analysis 22.0.1

Released on June 7, 2022


  • Updated the login method so login happens through a browser when uploading to Ingenuity Pathway Analysis using the Pathway Analysis tool.


Ingenuity Pathway Analysis 22.0

Released on January 11, 2022

Updated to be compatible with with CLC Genomics Workbench 22 and CLC Genomics Server 22.

New features

Import Expression Data
  • A new Import Expression Data tool is now available. It takes an expression matrix as input and creates an expression track per entry in the matrix. When running the tool as part of a workflow metadata can be associated to the expression tracks enabling end-to-end processing using downstream RNA-seq analysis tool.
  • A new workflow Analyze Count Matrix and Upload Comparison to IPA has been added to the plugin. It takes an expression matrix and accompanying metadata, performs differential expression analysis and directly uploads the statistical comparisons to IPA.


  • The Ingenuity Pathway Analysis workflows have been moved to a folder called IPA workflows in the Template Workflows toolbox.
  • Changed the Pathway Analysis command line tool command from ingenuity_pathway_new_analysis to ingenuity_pathway_analysis after removal of the Pathway Analysis (Legacy) tool.

Bug fixes

  • Fixed an issue where entering wrong IPA password when uploading more than 2 samples could make IPA upload hang.


  • Pathway Analysis (Legacy)


Ingenuity Pathway Analysis 21.0.1

Released on April 27, 2021


  • Minor improvements

Bug fixes

  • When a feature (gene or transcript) has a standard p-value, but a missing Bonferroni or FDR value, the missing values are set to 1.0 prior to upload. This fixes an issue where features with missing values were not used in IPA analyses launched from the plugin.
  • Fixed an issue affecting the Pathway Analysis tool, where upload of statistical comparison tables sometimes failed with an error about identifier types. This bug affected upload of Mouse and Rat datasets from the Single Cell Analysis Module.


Ingenuity Pathway Analysis 21.0

Released on January 12, 2021

Updated to be compatible with with CLC Genomics Workbench 21 and CLC Genomics Server 21.



Ingenuity Pathway Analysis 20.0

Released on December 11, 2019

Updated to be compatible with with CLC Genomics Workbench 20 and CLC Genomics Server 20.


Entering ‘IPA’ in the Quick launch search field now also shows the ‘Pathway Analysis’ tool

Ingenuity Pathway Analysis 2.4

Released on November 28, 2018

Updated to be compatible with with CLC Genomics Workbench 12 and CLC Genomics Server 11.

Ingenuity Pathway Analysis 2.3

Released on November 28, 2017

Ingenuity Pathway Analysis 2.2.1

Released on July 6th, 2017

Ingenuity Pathway Analysis 2.2

Released on March 2nd, 2017

Updated for compatibility with new workbench and server releases.

Ingenuity Pathway Analysis 2.1

Released on March 31, 2016