HotNet

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Welcome to the Google Group for HotNet, an algorithm for finding significantly altered subnetworks in a large gene interaction network developed by Raphael Lab at Brown University. Please post any questions you may have while using HotNet here. For more information on HotNet, see the project page and the source code on GitHub. You can always download the latest version of HotNet from the releases page.

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12/23/23

Does Hierarchical HotNet allow self-loop edge in the network?

Hi, I have a big PPI network with a lot of self loops, which are actually homodimer complexes. But

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Does Hierarchical HotNet allow self-loop edge in the network?

Hi, I have a big PPI network with a lot of self loops, which are actually homodimer complexes. But

12/23/23

10/24/22

Hierarchical Hotnet Consensus

Hello support team, Performing the consensus generates blank documents. Ran the example data and it

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Hierarchical Hotnet Consensus

Hello support team, Performing the consensus generates blank documents. Ran the example data and it

10/24/22

5/29/22

unable to understand the results

Hi Iam unable to understand the results, can anyone please help me to analyze it? Thanks

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unable to understand the results

Hi Iam unable to understand the results, can anyone please help me to analyze it? Thanks

5/29/22

3/3/22

Questions about installation or alternative packages

Hello, I've been having a hell of a time trying to get Hierarchical Hotnet running on OSX, given

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Questions about installation or alternative packages

Hello, I've been having a hell of a time trying to get Hierarchical Hotnet running on OSX, given

3/3/22

7/15/21

Hello, I'm new to Hierarchical HotNet and have a question: I'm trying to run the example

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Hello, I'm new to Hierarchical HotNet and have a question: I'm trying to run the example

7/15/21

3/25/21

p-value not significant in hierarchical-hotnet

Hi Matt, I applied gene data with customized scores on hint+hi2012, irefindex9, and multinet

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p-value not significant in hierarchical-hotnet

Hi Matt, I applied gene data with customized scores on hint+hi2012, irefindex9, and multinet

3/25/21

Nazli Kocatug (Alumni)

7/15/20

Hello, I'm new to HotNet and I have trouble with calculating similarity matrix, the error that I

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Hello, I'm new to HotNet and I have trouble with calculating similarity matrix, the error that I

7/15/20

5/8/20

Reproducing the experiments (running time)

It would have been great as well if anybody could share ready-to-use data for visualization. On

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Reproducing the experiments (running time)

It would have been great as well if anybody could share ready-to-use data for visualization. On

5/8/20

5/4/20

Error running HotNet2 (succesfully ran makeNetworkFiles and makeHeatFile)

Any advice would be very much appreciated - I successfully ran makeNetworkFiles.py and makeHeatFile.

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Error running HotNet2 (succesfully ran makeNetworkFiles and makeHeatFile)

Any advice would be very much appreciated - I successfully ran makeNetworkFiles.py and makeHeatFile.

5/4/20

4/29/20

Error with compilation of C / Fortran extensions

I hit errors trying to compile the fortran and C extensions as described in the README. Please let me

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Error with compilation of C / Fortran extensions

I hit errors trying to compile the fortran and C extensions as described in the README. Please let me

4/29/20

Güngör Budak, Matthew Reyna3

11/19/19

Any preprocessing for iRefIndex 15.0 used in Hierarchical HotNet?

Hi Matt, Thanks. Could you please have a look how I attempt to do it here: https://gist.github.com/

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Any preprocessing for iRefIndex 15.0 used in Hierarchical HotNet?

Hi Matt, Thanks. Could you please have a look how I attempt to do it here: https://gist.github.com/

11/19/19

Jeffrey Brabec, Matthew Reyna2

9/15/19

Parallelizing Hierarchical HotNet

Hi Jeff, Good question. The parts of Hierarchical HotNet in the construct_similarity_matrix_step.py

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Parallelizing Hierarchical HotNet

Hi Jeff, Good question. The parts of Hierarchical HotNet in the construct_similarity_matrix_step.py

9/15/19

Jeffrey Brabec, Matthew Reyna2

9/12/19

Incorporating the edge weights of my network into Hierarchical HotNet analysis

Hi Jeff, From your question, I assume that your network is both weighted and directed. The network

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Incorporating the edge weights of my network into Hierarchical HotNet analysis

Hi Jeff, From your question, I assume that your network is both weighted and directed. The network

9/12/19

Shivangi Agarwal, Matthew Reyna4

6/29/19

Change of parameters for statistical significance

Hi Shivangi, More permutations are better, but they will not substantially change the p-values.

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Change of parameters for statistical significance

Hi Shivangi, More permutations are better, but they will not substantially change the p-values.

6/29/19

Joshua Cook, matthe...@brown.edu4

3/20/19

Hierarchical HotNet: What to do with permitted network files?

Hi Josh, Please feel free to do so. I tried to make the example about as simple as possible by

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Hierarchical HotNet: What to do with permitted network files?

Hi Josh, Please feel free to do so. I tried to make the example about as simple as possible by

3/20/19

1/17/19

Hello, I run hotnet2, and would like to know whether you recommend to do correct the Pvalues obtained

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Hello, I run hotnet2, and would like to know whether you recommend to do correct the Pvalues obtained

1/17/19

Akos T, matthe...@brown.edu2

12/19/18

Connected components and sparse heat inputs

Hi Akos, Thanks for your questions! For your first question, HotNet2 is able to infer relationships

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Connected components and sparse heat inputs

Hi Akos, Thanks for your questions! For your first question, HotNet2 is able to infer relationships

12/19/18

Lorenzo, matthe...@brown.edu7

10/25/18

SegFault due to nx.to_numpy_matrix, using STRING

Hi Matt, I am sorry the last part of my last post was not very clear: my experiments were always made

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SegFault due to nx.to_numpy_matrix, using STRING

Hi Matt, I am sorry the last part of my last post was not very clear: my experiments were always made

10/25/18

Joshua Cook, matthe...@brown.edu5

10/23/18

"list index out of range" during Network Preparation

Hi Matt, That did the trick! It was a missing value on one line of the gene index file. I'm not

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"list index out of range" during Network Preparation

Hi Matt, That did the trick! It was a missing value on one line of the gene index file. I'm not

10/23/18

10/7/18

HotNet2 hangs when using multiple cores

There is an issue with my setup when trying to run Hotnet2 with multiple cores. The makeNetworkFiles.

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HotNet2 hangs when using multiple cores

There is an issue with my setup when trying to run Hotnet2 with multiple cores. The makeNetworkFiles.

10/7/18

seng...@gmail.com, matthe...@brown.edu3

9/27/18

nature genetic paper supplemental pdf file damaged

Thanks, Matt. This time works! Best, Sen 在 2018年9月26日星期三 UTC-7下午4:51:27，matthe...@brown.edu写道： Hi Sen

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nature genetic paper supplemental pdf file damaged

Thanks, Matt. This time works! Best, Sen 在 2018年9月26日星期三 UTC-7下午4:51:27，matthe...@brown.edu写道： Hi Sen

9/27/18

Shivangi Agarwal, matthe...@brown.edu10

8/11/18

P-value not significant

Hi Shivangi, You have P-values P < 0.05 for k = 4, 8, 9, 10, which means that there are

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P-value not significant

Hi Shivangi, You have P-values P < 0.05 for k = 4, 8, 9, 10, which means that there are

8/11/18

Armand Bankhead, matthe...@brown.edu2

8/1/18

hotnet2 consensus permutations

Hi Armand, Apologies -- this is a bug that arises when the numbers of heat permutations and consensus

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hotnet2 consensus permutations

Hi Armand, Apologies -- this is a bug that arises when the numbers of heat permutations and consensus

8/1/18

mrfox, … Armand Bankhead5

7/27/18

Thanks for your response! On Saturday, July 7, 2018 at 9:46:20 AM UTC-4, matthe...@brown.edu wrote:

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Thanks for your response! On Saturday, July 7, 2018 at 9:46:20 AM UTC-4, matthe...@brown.edu wrote:

7/27/18

qyw...@gmail.com, matthe...@brown.edu2

7/20/18

Erorr running makeNetworkFiles.py in paper/paper_commands.sh

Hi Qian, Most likely, this error occurred because you have an older version of NumPy, which is a

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Erorr running makeNetworkFiles.py in paper/paper_commands.sh

Hi Qian, Most likely, this error occurred because you have an older version of NumPy, which is a

7/20/18

yingh...@hotmail.com, matthe...@brown.edu11

6/2/18

Hi Matt, Thanks for you reply! After I got a list of subnetworks, my goal is to calculate the heat

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Hi Matt, Thanks for you reply! After I got a list of subnetworks, my goal is to calculate the heat

6/2/18

yingh...@hotmail.com, matthe...@brown.edu5

5/25/18

Warning massage

Sure, thanks a lot Matthew! On Friday, May 25, 2018 at 2:07:56 AM UTC+1, matthe...@brown.edu wrote:

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Warning massage

Sure, thanks a lot Matthew! On Friday, May 25, 2018 at 2:07:56 AM UTC+1, matthe...@brown.edu wrote:

5/25/18

Shivangi Agarwal, matthe...@brown.edu15

5/5/18

I am having 96GB RAM, out of which only 14% is used. I don't know what is the problem, also it is

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I am having 96GB RAM, out of which only 14% is used. I don't know what is the problem, also it is

5/5/18

Subanshi Kumari, matthe...@brown.edu4

4/30/18

Coverage and consensus subnetwork

Ya But I have used mutation data (snv file) to generate heat score using makeheatfile.py. On Sunday,

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Coverage and consensus subnetwork

Ya But I have used mutation data (snv file) to generate heat score using makeheatfile.py. On Sunday,

4/30/18

Shivangi Agarwal, matthe...@brown.edu4

4/15/18

Network permutations

Hi Shivangi, The choice of the delta parameter determines the sizes of the HotNet2 subnetworks. I was

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Network permutations

Hi Shivangi, The choice of the delta parameter determines the sizes of the HotNet2 subnetworks. I was

4/15/18

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