cangermueller/deepcpg

Issues

• Download links for example data broken

  #34 opened 2 years ago by Mr-Pepe
  0

• pip install deepcpg does not install tensorflow.

  #43 opened 2 years ago by shawarden
  0

• pip install deepcpg => bad interpreter: /anaconda3/envs/deepcpg/bin/python: no such file or directory

  #42 opened 2 years ago by shawarden
  0

• Negative strand index input

  #41 opened 2 years ago by yxwucq
  0

• Recommendations for using in Tumor Normal scenario

  #40 opened 3 years ago by harish0201
  0

• Can't calculate the pair potential

  #39 opened 4 years ago by 1920993165
  0

• keras/tensorflow version incompatibility

  #38 opened 4 years ago by sameelab
  0

• keras / tensorflow version compatibility

  #37 opened 5 years ago by rekham1077
  2

• Fails CpG module training

  #36 opened 5 years ago by yoramzarai
  0

• Problem with setup.sh when downloading cpg data

  #35 opened 5 years ago by yoramzarai
  1

• CpG sites in the negative strand

  #33 opened 5 years ago by yasin-chop
  3

• Error in train.sh

  #32 opened 5 years ago by yasin-chop
  1

• Example data not accessible

  #31 opened 5 years ago by yasin-chop
  1

• Models in the zoo are not accessible

  #30 opened 5 years ago by yasin-chop
  0

• impute CpG values for gene by cell matrix

  #29 opened 5 years ago by shengyongniu
  1

• Unable to train joint model from pretrained cpg and dna model with tensorflow backend

  #28 opened 5 years ago by snajder-r
  1

• GPU utility in training only about 25%

  #27 opened 5 years ago by snajder-r
  1

• This software can only predict the methylation status not the exact methylation level right

  #26 opened 5 years ago by sixone11
  0

• Can you provide pre-trained models from the DeepCpG model zoo

  #25 opened 6 years ago by Chamemee
  0

• CpG profiles file not found

  #24 opened 6 years ago by pegahmavaee
  4

• PCA of learnt motifs by DeepCpG

  #23 opened 6 years ago by janewangsmile
  0

• erros and warnings

  #22 opened 6 years ago by PoisonAlien
  5

• Error in dcpg_train.py

  #21 opened 6 years ago by timpeters82
  3

• Error in execution of File fine_tune/index.ipynb

  #20 opened 7 years ago by Abhishek019
  1

• Error filter

  #16 opened 7 years ago by frankmarab
  5

• Cannot open the deep_cpg/notebooks/basics/index.ipynb

  #18 opened 7 years ago by JieYang031
  1

• No access to ./data/anno.zip on the server

  #17 opened 7 years ago by JieYang031
  1

• ValueError: If printing histograms, validation_data must be provided, and cannot be a generator.

  #13 opened 7 years ago by AgentLjc
  11

• AttributeError: 'list' object has no attribute 'get_shape' when building model

  #15 opened 7 years ago by ajsteele
  1

• Installation

  #2 opened 7 years ago by AhmedJutt
  0

• Question about DeepCpG

  #3 opened 7 years ago by daquang
  7

• AttributeError: 'module' object has no attribute 'WeightRegularizer'

  #6 opened 7 years ago by PapaMadeleine2022
  1

• a problem

  #7 opened 7 years ago by PapaMadeleine2022
  1

• can not find dcpg_eval_perf.Rmd

  #8 opened 7 years ago by PapaMadeleine2022
  1

• confused on y and z in 'deepcpg/evaluate.py/evaluate(y, z, mask=CPG_NAN, metrics=CLA_METRICS)'

  #9 opened 7 years ago by PapaMadeleine2022
  1

• how to test only one cell?

  #10 opened 7 years ago by PapaMadeleine2022
  1

• Keras/Tensorflow combatible versions

  #14 opened 7 years ago by eathieniti
  2

• Fine tuning joint model doesn't seem to work.

  #12 opened 7 years ago by Bonder-MJ
  2

• Error in dcpg_eval.py: TypeError: len() of unsized object

  #11 opened 7 years ago by hui-tony-zk
  1

• Invalid file path or buffer object type: <class 'deepcpg.data.utils.GzipFile'>

  #4 opened 7 years ago by dnaase
  10

• can you provide datasets?

  #5 opened 8 years ago by PapaMadeleine2022
  2

• Error running CpG model

  #1 opened 8 years ago by hui-tony-zk
  3