GenePattern Team Blog


GenePattern needs your support

Posted on Thursday, April 25, 2024 at 03:50PM by GenePattern Team

If you are a GenePattern user, we would greatly appreciate your help in continuing this resource.

We are preparing a grant proposal to NCI's Information Technology for Cancer Research program for the sustainment of the GenePattern server and GenePattern Notebooks. We would greatly appreciate your email of support to accompany …

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GenePattern Coverage and Support December 23, 2021 - January 2, 2022

Posted on Tuesday, December 21, 2021 at 11:25AM by Barbara Hill

From December 23, 2021, through January 2, 2022, the GenePattern team will be out of the office for our annual holiday closing. During this time, the GenePattern and GenePattern Notebook servers and repositories will remain up. We will be monitoring them and, should anything happen to disrupt service, we will …

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End of Support for GParc

Posted on Thursday, December 09, 2021 at 03:47PM by Barbara Hill

As of December 13, 2021, GParc (GenePattern Archive) is no longer supported, and the website has been archived.

The modules themselves are still available for install from the GParc module repository.

Documentation for most* of the modules is archived in this public GitHub repository.

*module doc which was hosted on …

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End of support for modules using the deprecated GenePattern patch mechanism.

Posted on Monday, December 06, 2021 at 01:15PM by Barbara Hill

As of GenePattern 3.9_21.12_b373 the GenePattern "patch mechanism" for installing support libraries for modules has been deprecated, in favor of the current best practice of creating or providing Docker containers for modules to run in.

This meant that a number of older, no longer supported modules have officially …

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End of support for Cufflinks suite of modules

Posted on Thursday, October 28, 2021 at 01:52PM by Barbara Hill

The Cufflinks suite of modules is no longer under active development and is therefore deprecated. 

The Cufflinks suite of modules includes:

  • Cufflinks
  • Cuffcompare
  • Cuffmerge
  • Cuffdiff
  • CufflinksCuffmergePipeline (and the CufflinksWrapperPipeline)

It is no longer available on any of our servers or module repositories.

The module zip files and documentation are now …

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