MiraldiLab/maxATAC

Issues

• Invalid Interval Bounds Error When Training

  #46 opened 3 years ago
  0

• Reverse_complement training flag

  #45 opened 3 years ago
  2

• Finalize maxATAC v1 ATAC-seq data

  #42 opened 3 years ago
  2

• Issue with Loading Models during Prediction. Clash between keras and tensorflow.keras

  #41 opened 3 years ago
  1

• Issue with plotting models. Potential clash between keras and tf.keras modules

  #40 opened 3 years ago
  1

• Epoch Selection: Performance using chr 2 Training Cell Line AUPR vs Performance using Validation Dice Coefficient

  #35 opened 4 years ago
  0

• Stranded Prediction Benchmarking

  #34 opened 4 years ago
  0

• maxATAC install issues on local machines

  #33 opened 3 years ago
  7

• Test bowtie2 alignment vs STAR

  #32 opened 4 years ago
  1

• Bayesian Optimization

  #31 opened 4 years ago
  0

• Train models using the complement strand sequence and reverse orientation

  #30 opened 4 years ago
  5

• GPU not working with develop_ROI

  #28 opened 3 years ago
  3

• Troubleshoot min-max normalization and differences in max values across chromosomes

  #24 opened 4 years ago
  10

• Balancing ATAC-seq and ChIP-seq examples while training

  #22 opened 4 years ago
  8

• Whole genome prediction, ROI based prediction, and select chromosome prediction

  #19 opened 4 years ago
  0

• Snakemake workflow for train, validate, benchmark

  #17 opened 4 years ago
  1

• Better methods for model selection

  #16 opened 4 years ago
  1

• Additional Benchmarking Features for Binary and Quantitative Predictions

  #15 opened 4 years ago
  0

• Full binary models

  #14 opened 4 years ago
  1

• Test interpretation code with a full model set

  #13 opened 3 years ago
  0

• Test training models using stranded ATAC-seq signal

  #12 opened 3 years ago
  0

• Create a simple method to use average ChIP-seq signal to predict TF binding

  #11 opened 4 years ago
  1

• Can we supplement our ATAC models with DHS?

  #10 opened 4 years ago
  3

• Make average signal optional

  #9 opened 4 years ago
  1

• Test different Tn5 signal window sizes with binary and quantitative models

  #8 opened 4 years ago
  3