Selene (sequence-based deep learning package)

Contact owners and managers

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Google group for users of Selene (https://github.com/FunctionLab/selene).

If you have found a bug or have a feature request, please post an issue here: https://github.com/FunctionLab/selene/issues

Post in this group if you have questions about the package, case studies, or model development.

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Kamel MEHDI

6/8/24

Reference sequence for Drought Tolerance prediction using selene-sdk

Hello everybody I am a beginner user with Selene-sdk and I want to develop a model (Deep-Learning)

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Reference sequence for Drought Tolerance prediction using selene-sdk

Hello everybody I am a beginner user with Selene-sdk and I want to develop a model (Deep-Learning)

6/8/24

Marcel Mück

11/29/23

Running selene wih the original deepSEA model

Hello everybody, I was going through the instructions in `tutorials/variants_and_visualizations/

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Running selene wih the original deepSEA model

Hello everybody, I was going through the instructions in `tutorials/variants_and_visualizations/

11/29/23

Kamel MEHDI

11/25/23

Need Help to Install selene-sdk

Hello everybody I need your help to install selene-sdk on windows 10 In fact, when running pip

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Need Help to Install selene-sdk

Hello everybody I need your help to install selene-sdk on windows 10 In fact, when running pip

11/25/23

haicheng li

3/15/23

selene-sdk install

The installation of selene-sdk is not very convenient, "conda install -c bioconda selene-sdk

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selene-sdk install

The installation of selene-sdk is not very convenient, "conda install -c bioconda selene-sdk

3/15/23

Miguel Atencia, chen.ka...@gmail.com5

8/22/22

Is selene-sdk still in channel bioconda?

It works with pip. I have re-tried using only command-line: conda create --name selpy python=3.7

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Is selene-sdk still in channel bioconda?

It works with pip. I have re-tried using only command-line: conda create --name selpy python=3.7

8/22/22

goutha...@gmail.com, chen.ka...@gmail.com2

8/19/22

Sei, Selene-SDK, RandomPositionsSampler

Hi Goutham, So sorry for the late response - next time don't hesitate to follow-up as I often

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Sei, Selene-SDK, RandomPositionsSampler

Hi Goutham, So sorry for the late response - next time don't hesitate to follow-up as I often

8/19/22

Weichen Song, chen.ka...@gmail.com2

3/22/22

Can seqweaver take sequence (.fa) instead of variant (.vcf) as input?

Hi Weichen, Thank you for your message! You cannot input a FASTA file to `vep_cli.py` but you can

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Can seqweaver take sequence (.fa) instead of variant (.vcf) as input?

Hi Weichen, Thank you for your message! You cannot input a FASTA file to `vep_cli.py` but you can

3/22/22

Nicolas Barbera, Jian Zhou3

10/25/21

Integrating Selene-built Model with ExPecto

Sorry correction to the sequence encodings I mentioned from last message, it should actually be (

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Integrating Selene-built Model with ExPecto

Sorry correction to the sequence encodings I mentioned from last message, it should actually be (

10/25/21

Claire Vink

9/21/21

Epistasis crops

Hi Kathy, Currently, I am writing my master thesis at Tilburg University and the aim of my thesis is

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Epistasis crops

Hi Kathy, Currently, I am writing my master thesis at Tilburg University and the aim of my thesis is

9/21/21

Ryan Friedman

9/5/21

Multi-class classification/one-hot encoded labels

Hi Kathy et al., I'm trying to train my neural net to do multi-class classification, ie I have K

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Multi-class classification/one-hot encoded labels

Hi Kathy et al., I'm trying to train my neural net to do multi-class classification, ie I have K

9/5/21

Ryan Friedman, chen.ka...@gmail.com3

8/23/21

Potential issue with reproducibility

Thanks for looking into this Kathy! The lines you provided solved the problem, although I didn't

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Potential issue with reproducibility

Thanks for looking into this Kathy! The lines you provided solved the problem, although I didn't

8/23/21

goutha...@gmail.com, … Christopher Park5

6/3/21

Seqweaver DIS vs RBP dysregulation

Hi Chris, Thanks for the explanation. - Goutham A On Tuesday, 1 June 2021 at 15:35:49 UTC+1 cp...@

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Seqweaver DIS vs RBP dysregulation

Hi Chris, Thanks for the explanation. - Goutham A On Tuesday, 1 June 2021 at 15:35:49 UTC+1 cp...@

6/3/21

Ryan Friedman, … Jian Zhou9

3/15/21

NotImplementedError with PyTorch

Hi Ryan, Yes - agree that using one-hot encoding and change the custom loss function to handle it is

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NotImplementedError with PyTorch

Hi Ryan, Yes - agree that using one-hot encoding and change the custom loss function to handle it is

3/15/21

Vibha R, chen.ka...@gmail.com2

12/28/20

Attribute Error when using Random Positions Sampler

Hi, thanks for your post. Would you be able to repost this to our Github issues? https://github.com/

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Attribute Error when using Random Positions Sampler

Hi, thanks for your post. Would you be able to repost this to our Github issues? https://github.com/

12/28/20

goutha...@gmail.com, Jian Zhou2

12/21/20

seqweaver scores

Hi Goutham, As you mentioned, since seqweaver predicts effects on RNA-binding proteins it does not

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seqweaver scores

Hi Goutham, As you mentioned, since seqweaver predicts effects on RNA-binding proteins it does not

12/21/20

goutha...@gmail.com, chen.ka...@gmail.com3

12/21/20

visualize the feature importance scores - Seqweaver

Thanks Kathy for pointing to these useful resources. On Tuesday, 24 November 2020 at 19:41:45 UTC+1

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visualize the feature importance scores - Seqweaver

Thanks Kathy for pointing to these useful resources. On Tuesday, 24 November 2020 at 19:41:45 UTC+1

12/21/20

Stephen Wang, Kathy Chen2

8/7/20

questions about variant effect prediction

Hi Stephen, Thanks so much for your post! 1. The tutorials are only compatible with the version of

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questions about variant effect prediction

Hi Stephen, Thanks so much for your post! 1. The tutorials are only compatible with the version of

8/7/20

atla goutham, … Jian Zhou10

7/12/20

Interpretation of insilico mutagenesis

Hi Zofie, If you want to use the DIS score as is published, it needs to be using the DeepSEA ASD

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asdbrowser

dis

Interpretation of insilico mutagenesis

Hi Zofie, If you want to use the DIS score as is published, it needs to be using the DeepSEA ASD

7/12/20

Zofie Lin, … Kathy Chen8

7/2/20

runing with selene_cli

Hi Zofie, I used the same YAML file (I think the tabix file `.bed.gz` name was wrong so I updated

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runing with selene_cli

Hi Zofie, I used the same YAML file (I think the tabix file `.bed.gz` name was wrong so I updated

7/2/20

Dewan Shrestha, … Kathy Chen7

6/3/20

deesea_TF_intervals

Hi! Thanks for your question. This kind of "interval restriction" is described in the

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deesea_TF_intervals

Hi! Thanks for your question. This kind of "interval restriction" is described in the

6/3/20

Clive Darwell, … Kathy Chen19

3/17/20

using CUDA on HPC

Sounds good, happy to help when you have more updates on this!

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using CUDA on HPC

Sounds good, happy to help when you have more updates on this!

3/17/20

Dat Duong, Kathy Chen2

2/7/20

Where in code and how should I change Selene pipeline to use Kmer instead of raw sequences?

Hi Dat, I'd probably suggest using the MatFileSampler in Selene and generating your own custom

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Where in code and how should I change Selene pipeline to use Kmer instead of raw sequences?

Hi Dat, I'd probably suggest using the MatFileSampler in Selene and generating your own custom

2/7/20

Dat Duong, Kathy Chen2

1/11/20

Using the same evaluation code on my own model

Sorry I totally missed this post & only saw it today when I re-reviewed the google groups. Yes,

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Using the same evaluation code on my own model

Sorry I totally missed this post & only saw it today when I re-reviewed the google groups. Yes,

1/11/20

Dat Duong, Jian Zhou2

12/20/19

How to load a model back to continue training?

Hi Dat, You can provide your previous model by specifying checkpoint_resume in selene_sdk.TrainModel

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How to load a model back to continue training?

Hi Dat, You can provide your previous model by specifying checkpoint_resume in selene_sdk.TrainModel

12/20/19

Dat Duong, Kathy Chen3

12/20/19

Running code on danQ.py

Thanks. I sent you a reply in my gmail by using "reply all" but I guess it didn't show

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Running code on danQ.py

Thanks. I sent you a reply in my gmail by using "reply all" but I guess it didn't show

12/20/19

Katha Korgaonkar, Kathy Chen11

9/11/19

Running Case 2 on Personal Data

I think I was finally able to get it. Thank you so much for all your help Kathy!!

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Running Case 2 on Personal Data

I think I was finally able to get it. Thank you so much for all your help Kathy!!

9/11/19

atla goutham, Kathy Chen3

8/6/19

Selene with different samplers

Thanks for the answer. I will check those plots once it finishes running.

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Selene with different samplers

Thanks for the answer. I will check those plots once it finishes running.

8/6/19