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Hi dear Gitools user.

Please use this mailing list to ask questions you may have specific questions regarding Gitools and it's use. For more genereal (bioinformatics) problems, consider if BioStars may be the appropriate site to ask for help.

Thanks

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1/24/22

Connection closed

Hi! I tried to download the GO Biological Processes module but I got an error massage (please find

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Connection closed

Hi! I tried to download the GO Biological Processes module but I got an error massage (please find

1/24/22

archana bhardwaj2

1/22/18

Sample level enrichment analysis - sample data

Hi, subtypes have been shown in vedio available at https://www.youtube.com/watch?v=EADA6TsGrVw Please

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Sample level enrichment analysis - sample data

Hi, subtypes have been shown in vedio available at https://www.youtube.com/watch?v=EADA6TsGrVw Please

1/22/18

archana bhardwaj, Jordi Deu5

1/22/18

Error in annotation and modules downloading

Hi Archana, there is already an open issue reporting this problem [1]. The problem it's that KEGG

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Error in annotation and modules downloading

Hi Archana, there is already an open issue reporting this problem [1]. The problem it's that KEGG

1/22/18

cgib...@email.mmc.edu, Jordi Deu5

1/8/18

Hi, after installing Anaconda, you run the Anaconda Navigator, you add the "bbglab" channel

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Hi, after installing Anaconda, you run the Anaconda Navigator, you add the "bbglab" channel

1/8/18

Varun Gupta, Jordi Deu2

12/15/17

gitools on ubuntu

Hi Varun, gitools requires Java 7 on your system. It gives some problems with Java 8 and the current

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gitools on ubuntu

Hi Varun, gitools requires Java 7 on your system. It gives some problems with Java 8 and the current

12/15/17

João Luiz Baldim, Jordi Deu3

12/20/16

Importing other type of data than genomic data.

Thank you very much for your answer! This software is very nice for my purposes due to the

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Importing other type of data than genomic data.

Thank you very much for your answer! This software is very nice for my purposes due to the

12/20/16

lukyluk...@gmail.com, jord...@irbbarcelona.org2

11/28/16

Import data from Excel file

Hi Luca, Gitools can directly open an excel file if you have your data in a "table layout"

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Import data from Excel file

Hi Luca, Gitools can directly open an excel file if you have your data in a "table layout"

11/28/16

7/8/16

Hi, I've been trying to visualize the Pancancer 12 supermatrix data on gitools. As recommended I

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Hi, I've been trying to visualize the Pancancer 12 supermatrix data on gitools. As recommended I

7/8/16

Karolina Modzelewska, Jordi Deu-Pons2

6/22/16

Deleted rows after uploading to Gitools - file size problem?

Hi Karolina, may be you have duplicated names (protein ids) as row identifiers. For example if you

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Deleted rows after uploading to Gitools - file size problem?

Hi Karolina, may be you have duplicated names (protein ids) as row identifiers. For example if you

6/22/16

JL Villanueva, Michael P Schroeder3

5/27/16

modify heatmap colors

Hi You may also use the menu: Edit -> Value Layers -> Layer of Choice... -> Color Sscale

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modify heatmap colors

Hi You may also use the menu: Edit -> Value Layers -> Layer of Choice... -> Color Sscale

5/27/16

Sebastian Lau, … Jordi Deu-Pons4

2/18/16

Can someone show me an example of column annotation file for heatmap?

Hi Sebastian, if done a small test with your annotations file and it seems to work. If you want 4

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Can someone show me an example of column annotation file for heatmap?

Hi Sebastian, if done a small test with your annotations file and it seems to work. If you want 4

2/18/16

George, Michael P Schroeder4

2/17/16

Z Score is None in Enrichment Analysis with KEGG pathway

So the the first problem is that you have less than 20 data points per Module which leads (with the

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Z Score is None in Enrichment Analysis with KEGG pathway

So the the first problem is that you have less than 20 data points per Module which leads (with the

2/17/16

setar...@gmail.com, Jordi Deu-Pons2

10/20/15

Gitools installation

Hi Mary, try to click one of the "gitools-?GB.bat" files that are in the "bin"

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Gitools installation

Hi Mary, try to click one of the "gitools-?GB.bat" files that are in the "bin"

10/20/15

Lydia Yao, Michael P Schroeder2

9/7/15

hierarchical clustering label

Hi Lydia Yes, as in the hierarchical clustering, at each step, the subjects are split into two groups

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hierarchical clustering label

Hi Lydia Yes, as in the hierarchical clustering, at each step, the subjects are split into two groups

9/7/15

5/6/15

[Inquiry] Running Gitools from command line in Linux system

Hi, We want to include gitools-enrichment into our analysis pipeline. But I cannot find detailed

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[Inquiry] Running Gitools from command line in Linux system

Hi, We want to include gitools-enrichment into our analysis pipeline. But I cannot find detailed

5/6/15

Soo Hee Lee, Michael P Schroeder2

1/12/15

Broken links to KEGG geneset enrichment analysis

Hi Soo Hee, Thanks for reporting, the links should now be working. Please take into account that the

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Broken links to KEGG geneset enrichment analysis

Hi Soo Hee, Thanks for reporting, the links should now be working. Please take into account that the

1/12/15

Michael P Schroeder

10/9/14

Re: [gitools-users] TCGA Brain Lower Grade Glioma samples

Hi PK Right now we have no further TCGA projects prepared as Gitools Heatmaps than the ones available

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Re: [gitools-users] TCGA Brain Lower Grade Glioma samples

Hi PK Right now we have no further TCGA projects prepared as Gitools Heatmaps than the ones available

10/9/14

Luca Zammataro, Michael P Schroeder3

9/24/14

TDM file format.

Many thanks Michael the TDM files that i cited is present in the gitools sample data directories.

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TDM file format.

Many thanks Michael the TDM files that i cited is present in the gitools sample data directories.

9/24/14

Jordi Deu-Pons, … Sarah Pohl6

5/27/14

Gitools and proxy settings

Hey Michael, I don't know... I have a desktop application, RescueTime, where I just enter the

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Gitools and proxy settings

Hey Michael, I don't know... I have a desktop application, RescueTime, where I just enter the

5/27/14

Sarah Pohl, Michael P Schroeder3

5/26/14

Enrichment Analysis with KEGG pathways

I see, thank you! I downloaded the pathway two weeks ago when I had the work laptop outside our

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Enrichment Analysis with KEGG pathways

I see, thank you! I downloaded the pathway two weeks ago when I had the work laptop outside our

5/26/14

Whijae Roh, … Jordi Deu-Pons4

5/16/14

Question about reordering or deleting row headers

Thanks a lot. It solved my issue. Best, Whijae Roh On Fri, May 16, 2014 at 3:14 AM, Jordi Deu-Pons

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Question about reordering or deleting row headers

Thanks a lot. It solved my issue. Best, Whijae Roh On Fri, May 16, 2014 at 3:14 AM, Jordi Deu-Pons

5/16/14

Will Lyon, Michael P Schroeder2

4/15/14

Mean expression calculations

Hi Will I am not quite sure what data you are working with. Are you talking about a heatmap available

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Mean expression calculations

Hi Will I am not quite sure what data you are working with. Are you talking about a heatmap available

4/15/14

nicole, Michael P Schroeder4

4/15/14

Problem running Gitools 2.1.1 on a Mac OSX 10.8.5 and Java 7v51

Oh ok! That's tricky. Thank you very much for reporting that! Michael On Tue, Apr 15, 2014 at 1:

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Problem running Gitools 2.1.1 on a Mac OSX 10.8.5 and Java 7v51

Oh ok! That's tricky. Thank you very much for reporting that! Michael On Tue, Apr 15, 2014 at 1:

4/15/14

Vasilios Zachariadis, Michael P Schroeder5

2/28/14

Gitools unresponsive on OSX10.9 with Java 7v51

We are not sure. One think it could be is the Look and Feel or some 3D options for Java or the OS. So

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Gitools unresponsive on OSX10.9 with Java 7v51

We are not sure. One think it could be is the Look and Feel or some 3D options for Java or the OS. So

2/28/14

Maarten van Gils, Michael P Schroeder2

12/4/13

Correlation analysis and clustering

Hi Maarten First, thanks for taking the time share the issue. It seems that you have stumbled upon a

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Correlation analysis and clustering

Hi Maarten First, thanks for taking the time share the issue. It seems that you have stumbled upon a

12/4/13

Doo-Sik Kong, Michael Schroeder4

11/4/13

problem with SLEA

Hi Doo-Sik Kong I am glad you could solve the issue. Best, Michael

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problem with SLEA

Hi Doo-Sik Kong I am glad you could solve the issue. Best, Michael

11/4/13

Mary Mangan, Michael P Schroeder3

10/1/13

2.0 error message

Yes, that's definitely the version I've got: http://screencast.com/t/1fOQBYz7W Just wanted to

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2.0 error message

Yes, that's definitely the version I've got: http://screencast.com/t/1fOQBYz7W Just wanted to

10/1/13

Junfeng Jiang, Jordi Deu-Pons2

8/13/13

values labeled on the heatmap

Hi Junfeng, we already have an open issue for this problem: https://github.com/gitools/gitools/issues

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values labeled on the heatmap

Hi Junfeng, we already have an open issue for this problem: https://github.com/gitools/gitools/issues

8/13/13

Junfeng Jiang, Nuria Lopez-Bigas2

8/2/13

how to lable the mutation freq. on the heatmap like the picture you offered on your website

Hi Jiang, In the web where you have seen this image, just click the launch button at the right. In

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how to lable the mutation freq. on the heatmap like the picture you offered on your website

Hi Jiang, In the web where you have seen this image, just click the launch button at the right. In

8/2/13

Toni Delorey, Christian Perez-Llamas3

7/19/13

File formatting issues

I pasted two images but seems that googlegroups doesn't like that. You have this: id SCER_t60

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File formatting issues

I pasted two images but seems that googlegroups doesn't like that. You have this: id SCER_t60

7/19/13

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