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Ingenuity Pathway Analysis plugin latest improvements

Ingenuity Pathway Analysis 22.0.1

Released on June 7, 2022

Improvements

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.

Workflows

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.

Improvements

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.

Retirements

Pathway Analysis (Legacy)

Ingenuity Pathway Analysis 21.0.1

Released on April 27, 2021

Improvements

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.

Improvement

The Ingenuity Pathways Analysis Plugin for CLC Genomics Workbench now supports the choice between upload to the IPA US server and the IPA China server.

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.

Improvements

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

The choice of analysis reference been moved from the upload parameter dialogue page to its own dialogue page in the wizard. This is more appropriate as this option is only relevant for the analysis step. The user is now asked to explicitly choose between two possible options (user data or IPA knowledge base).
The headers of the table that is uploaded to IPA have been corrected to display their original full name.
Improved error message describing why the data could not be uploaded to IPA.
The Reference Data Set name and version number used in the mapping are now included in the notes uploaded to IPA.
Legacy Pathway Analysis tool moved to the Legacy toolbox folder.

Ingenuity Pathway Analysis 2.2.1

Released on July 6th, 2017

Users can now choose between two possible reference for analysis in IPA: user data or IPA Knowledge Base.
The Reference Data Set name and version number used in the mapping are now included in the notes uploaded to IPA.
The headers of the table that is uploaded to IPA are now visible in IPA.
Improved error message describing why the data could not be uploaded to IPA.
The Legacy Pathway Analysis tool has been moved to the Legacy folder of the Toolbox.

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

The existing Pathway Analysis tool has been renamed to Pathway Analysis (legacy), and a new tool has been included with the name Pathway Analysis. The Pathway Analysis tool accepts data of the type Statistical Comparisons as input.
A Ready-to-Use workflow has been added to the plugin that allows multi-factorial statistical analysis and upload of the generated statistical comparisons to IPA, and graphical visualizations such as heat maps, PCA plots, and Venn diagrams.
Cutoffs can now be specified for how many features to upload and how many to analyze.
The number of target features for the pathway analysis can be specified in the wizard and as a result the system will pick the cutoff based on FC.
The project name field in the plugin wizard now accepts special characters.
The dataset and analysis names get as default the name of the dataset in the workbench with a date and time extension.
The option to choose t-test has been enabled in the Pathway Analysis (legacy) tool.
The Ingenuity Pathway Analysis Plugin is able to use the proxy settings specified in the Workbench preferences.