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Issues7 (7)

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kundajelab/ChromDragoNN

GRCh38 model

Hi, do you have a pretrained model based on GRCh38 ? Thanks Gianfilippo

• gianfilippo
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• 5
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• Opened 
  on Jul 16, 2021
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• #9

kundajelab/ChromDragoNN

Structure of dnase.chr.packbited.tar.gz data

Dear Kundaje lab, I m exploring the data associated with your paper Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts . I ...

• sb-vsfishman
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• 3
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• Opened 
  on Jun 4, 2021
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• #7

kundajelab/ChromDragoNN

ERROR: Not all intervals have the same length

Hi, I am trying to test your algorithm. I downloaded the data from the links you provide, and I am starting with the command you provide: python ./preprocess/make_accessibility_joblib.py --input /path/to/accessibility/file.tsv.gz ...

• gianfilippo
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• 9
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• Opened 
  on Jun 30, 2020
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• #6

kundajelab/ChromDragoNN

color2ctype is missing from tSNE notebook

Hello I was wondering if you can make the color2ctype labels available for the tSNE notebook plots? thank you, Omar

• ghost
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• 10
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• Opened 
  on May 2, 2020
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• #5

kundajelab/ChromDragoNN

Question about input matrix

Hi, if I want to train a model to predict binary accessibility in my own cell types of interest, can you provide some guidance for how to preprocess my data? Where do I input the binary matrix of accessibility ...

• chowdharyk
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• 7
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• Opened 
  on Jan 22, 2020
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• #4

kundajelab/ChromDragoNN

Make trained model available for prediction

I ve been trying to train the resnet.py model to predict accessibility from DNA sequence (on the provided DNAse-seq data). I ve ran into some issues (listed below). Is it possible for you to provide the ...

• jhammelman
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• 3
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• Opened 
  on Dec 17, 2019
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• #3

kundajelab/ChromDragoNN

what's the reason behind these filter and padding schemes?

Hello Surag, Thanks for the great paper and the codes! Really appreciate researchers share their work with their codes! I see that the code uses filter sets of either (3, 1) (7, 1) (1, 1). And if I understand ...

• ccchang0111
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• 2
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• Opened 
  on May 25, 2019
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• #2

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