Download iRegulon

Version 1.3:
------------

  * The selected transcription factor for each
    motif cluster in transcription factor view
    is now chosen deterministically.

Version 1.2:
------------

  * This version includes track discovery and a
    large motif collection with nearly 10K PWMs.

  * Cytoscape 3.1.x plugin:
      - bug fixes and adaptation to cytoscape 3.
      - new iregulon visual style.
      - edge color matching cluster color.

Version 0.97:
------------

  * Large motif collection with around 6K PWMs.
  * No track discovery.

>> Read Software License

iRegulon plugin for Cytoscape 2.8.x: released 12 February 2015

iRegulon plugin for Cytoscape 3.2.x: released 12 February 2015

Download version with Public PWMs (Cytoscape App Store)

Download version with Public PWMs and TRANSFAC PRO PWMs

Warning! Download this version only if you have a TRANSFAC Professional license.

Cytoscape 2.8.x

Cytoscape 3.2.x

Download source code

Our source code is now publicly available.

For Cytoscape 2.8.x :

Download version with Public PWMs
Download version with Public PWMs and TRANSFAC PRO PWMs

For Cytoscape 3.2.x :

Download version with Public PWMs
Download version with Public PWMs and TRANSFAC PRO PWMs

Software License Agreement

This Software is developed by and on behalf of the Laboratory of Computational Biology of the KU Leuven and is owned by the Katholieke Universiteit Leuven (hereinafter referred to as “KU LEUVEN"). By downloading or installing the Software you agree with the terms and conditions below.

Software License Agreement This Software is developed by and on behalf of the Laboratory of Computational Biology of the KU Leuven and is owned by the Katholieke Universiteit Leuven (hereinafter referred to as “KU LEUVEN”). By downloading or installing the Software you agree with the terms and conditions below. Article 1 - Definitions 1.1 “Software” shall mean the iRegulon Cytoscape plugin as available on the website http://iregulon.aertslab.org and via the Cytoscape App Store as jar file. The software that you install is the client of a client-server system whereby the client sends a request to a web server (for example, running at the KU Leuven). The request consists of a list of genes (i.e., a list of nodes in a Cytoscape network), along with parameters. The client receives the results of the motif/track discovery and motif2TF mapping as a table with motifs, tracks, candidate transcription factors, and predicted target genes. These results can be used to ‘annotate’ the active Cytoscape networks, and can be saved as text or irf format. 1.2 “Effective Date” shall mean the date on which you download or install the iRegulon Cytoscape plugin (as available on http://iregulon.aertslab.org and via the Cytoscape App store) on your system and which provide you access to the iRegulon webapplication. 1.3 “Non-commercial User” shall mean a person using the Software for non-commercial research purposes on its own behalf or on behalf of a legal entity. In case the Non-commercial User is acting on behalf of an entity, use of the Software is only permitted by the Non-Commercial User in the event the Software License Agreement is approved and signed by the authorized signatories of such legal entity and returned to KU LEUVEN. Article 2 - License 2.1 As long as you qualify as a Non-commercial User, KU LEUVEN hereby grants you a royalty-free, non-exclusive, non-transferable license to the Software supplied by KU LEUVEN for strictly internal, non-commercial research use only. 2.2 You acknowledge and agree that you may not use the Software for non-research and/or commercial purposes without first obtaining an appropriate license from KU LEUVEN. For the purposes of this Agreement “use for commercial purposes” shall include the use or transfer of the Software for a consideration as well as the use of the Software to support commercial activities including providing services with the Software to third parties. Any use of Software for commercial purposes shall be deemed a breach of this Agreement for which KU LEUVEN shall be entitled to whatever remedies it may have under law or equity, including recovery of any damages. 2.3 You shall not sublicense any of your rights to the Software. Neither will you transfer the Software to a third party, unless prior written agreement of KU LEUVEN has been obtained. Furthermore, you are not allowed to reverse engineer, decompile or disassemble the Software. 2.4 This Agreement does not grant or imply any right, title or license into or under any third party software (including but not limited to e.g. Cytoscape software) or intellectual property rights relating thereto. Article 3 - Ownership The Software is copyrighted and KU LEUVEN retains all title and ownership to the Software. Nothing in this Agreement shall preclude KU LEUVEN from entering into agreements with third parties concerning the Software. Article 4 - Publication Non-commercial User shall acknowledge KU LEUVEN as the owner of the Software and shall include a reference to the iRegulon publication and to KU LEUVEN in any manuscript describing data obtained using the Software. Article 5 - No Support This license does not entitle you to receive from KU LEUVEN technical support, telephone assistance, or enhancements or updates to the Software. Any support that may be given by KU LEUVEN on voluntary basis is provided “as is” and KU LEUVEN makes no representations or warranties of any type whatsoever, express or implied, regarding the provided support. Article 6 - Warranty 6.1 The Software is provided “as is” by KU LEUVEN without warranty of any kind, whether express or implied. KU LEUVEN specifically disclaims the implied warranties of merchantability and fitness for a particular purpose or that the use of the Software will not infringe any patents, copyrights or trademarks or other rights of third parties. The entire risk as to the quality and performance of the Software is borne by you. 6.2 Without prejudice to KU LEUVEN’s liability for damages caused by KU LEUVEN’s willful misconduct, KU LEUVEN shall not be liable for any loss, direct or indirect damage or other liability incurred by you or any third party in connection with the Software licensed by KU LEUVEN under this Agreement. Under no circumstances shall KU LEUVEN be liable for any direct, indirect, special, incidental, or consequential damages arising out of any performance of this Agreement, whether such damages are based on contract, tort or any other legal theory. Article 7 - Indemnification You will indemnify, defend and hold harmless KU LEUVEN, its directors, officers, employees and agents from and against all liability, losses, damages and expenses (including attorney’s fees and costs) arising out of any claims, demands, actions or other proceedings made or instituted by any third party against any of them and arising out of or relating to any breach of this Agreement by you, or any use or disclosure of the Software by you, unless such claims or liability result from KU LEUVEN’s willful misconduct. Article 8 - Term 8.1 This Agreement is effective from the Effective Date until you delete the Software and any and all related files from your computing system. This Agreement will terminate immediately without notice from KU LEUVEN if you fail to comply with any provision of this Agreement. KU LEUVEN may terminate this Agreement at any time by inactivating your access to the Software. 8.2 In case of termination the provisions of Article 3, 4, 6, and 7 shall remain in full force and effect. Article 9 - Miscellaneous 9.1 Any notice authorized or required to be given to KU LEUVEN under this Agreement shall be in writing and shall be deemed to be duly given if sent by registered post to: KU Leuven Research & Development, Waaistraat 6, B-3000 Leuven, Belgium with attention to IP Department. 9.2 The terms and conditions herein contained constitute the entire agreement between the Parties and supersede all previous agreements and understandings, whether oral or written, between the parties hereto with respect to the subject matter thereof. Article 10 - Disputes In the event of disputes in the interpretation and/or performance of this Agreement, the parties shall first undertake to settle their differences amicably. If no amicable settlement can be reached concerning the execution and/or interpretation of this Agreement, such conflict shall be brought before the courts of Leuven and Belgian Law shall be applicable.

Installation procedures

For Cytoscape 2.8.x :

Download the jar file
If necessary, uninstall older version of the plugin (Menu > Plugins > Manage Plugins, Delete old iRegulon plugin, restart Cytoscape)
Install the new iRegulon plugin (Menu > Plugins > Install Plugin from File)
Restart Cytoscape

For Cytoscape 3.2.x :

Download the jar file
If necessary, uninstall older version of the plugin (Menu > Apps > App manager > Currently installed > Uninstall old iRegulon plugin, restart Cytoscape)
Install the new iRegulon plugin (Menu > Apps > App manager > Install Apps > Install from File...)
Restart Cytoscape

Previous versions

Release v1.2 (track discovery and a large motif collection with nearly 10K PWMs).

Plugin:

For Cytoscape 2.8.x :

For Cytoscape 3.1.x :

Source code:

For Cytoscape 2.8.x :

For Cytoscape 3.1.x :

Download iRegulon

Download version with Public PWMs and TRANSFAC PRO PWMs

Download source code

Software License Agreement

Installation procedures

Previous versions

Release v1.2 (track discovery and a large motif collection with nearly 10K PWMs).

Plugin:

Source code:

Release v1.1 (first version submitted to Cytoscape App Store, "6K" motif collection, no track discovery):

Plugin:

Release v0.97 ("6K" motif collection, no track discovery):

Plugin: