MiraldiLab/maxATAC

Issues

• import error _OrderedEnqueuer_ tensorflow.keras.utils

  #129 opened 8 months ago by martinezvbs
  6

• `maxATAC` prepare with sc 10X ATAC

  #119 opened 2 years ago by daccachejoe
  2

• Change Path for

  #130 opened 8 months ago by Elfaba
  1

• Error on running prepare: subprocess.CalledProcessError

  #128 opened a year ago by Lozzard
  1

• pseudo-bulk

  #126 opened a year ago by drosop
  3

• keras error after installation

  #122 opened a year ago by sleepryansleep
  2

• Numpy compatibility for Tensorflow 2.5 and SHAP in interpreting analysis jobs

  #58 opened 3 years ago by XiaotingChen
  2

• Finalize Code Base

  #80 opened 2 years ago by FaizRizvi
  14

• pyBigWig values method does not take argument numpy=True

  #117 opened 2 years ago by tanjimin
  1

• Error on running predict: could not load dynamic library for tensorflow

  #115 opened 2 years ago by timothykoala
  1

• Question about training/testing celltypes

  #116 opened 2 years ago by ninashenker
  1

• Error on running prepare function - error while loading shared libraries: libncurses.so.5

  #114 opened 2 years ago by timothykoala
  2

• Remove hardcoded paths in `maxatac prepare` and in maxatac_data so users can provide custom chromosome sets

  #112 opened 2 years ago by tacazares
  6

• Make sure the maxATAC python package can be installed on python 3.7/3.8/3.9 on both Ubuntu and macOS

  #63 opened 2 years ago by michael-kotliar
  5

• What is the fourth column in the bed file the variants function produce?

  #111 opened 2 years ago by songzeji
  2

• Fix flags across functions for consistency

  #109 opened 2 years ago by tacazares
  0

• Improve `maxatac prepare`

  #107 opened 2 years ago by tacazares
  1

• variants_bed invalid int value

  #93 opened 2 years ago by hrayjones
  13

• bedGraphToBigWig: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

  #102 opened 2 years ago by tacazares
  1

• Best value to use for thresholds

  #91 opened 2 years ago by tacazares
  1

• Update peak centric prediction

  #77 opened 2 years ago by tacazares
  0

• Enhancements: sex chromosome predictions

  #83 opened 3 years ago by emiraldi
  2

• Add code for plots/update functions associated with `normalize`, `average`, `prepare`, and `benchmark`

  #108 opened 3 years ago by tacazares
  0

• Update `maxatac train` and optimize

  #101 opened 3 years ago by tacazares
  1

• Add tests and set up some Continuous Integration (CI)

  #104 opened 3 years ago by tacazares
  0

• Graphviz error with `maxatac train`

  #100 opened 3 years ago by tacazares
  0

• `maxatac prepare` erroring out at normalization

  #96 opened 3 years ago by codymowery
  2

• `maxatac prepare` issue processing scATAC-seq fragment files

  #97 opened 3 years ago by tacazares
  0

• Interesting observation with predictions: Blacklist update

  #90 opened 3 years ago by tacazares
  2

• train.md clarifications

  #89 opened 3 years ago by emiraldi
  0

• Installation issues with pyBigWig not finding numpy

  #87 opened 3 years ago by tacazares
  0

• docs/readme/peaks.md disconnect example / arguments

  #88 opened 3 years ago by emiraldi
  1

• Benchmarking: separate quantitative and binary evaluation

  #84 opened 3 years ago by emiraldi
  0

• Docker and install

  #65 opened 3 years ago by FaizRizvi
  16

• --agg options for benchmark.md

  #86 opened 3 years ago by emiraldi
  2

• default for noramlize.md

  #85 opened 3 years ago by emiraldi
  0

• Error in how area under the precision recall curve is calculated

  #54 opened 3 years ago by tacazares
  0

• Define the list of the commands a user will be able to run and what results they will produce

  #64 opened 3 years ago by michael-kotliar
  1

• Implement and document a way to retrieve the required reference data

  #66 opened 3 years ago by tacazares
  3

• OSC Node Crash invoked by Kernel Bug

  #56 opened 3 years ago by FaizRizvi
  1

• Optimize whole-genome prediction time

  #69 opened 3 years ago by tacazares
  1

• Optimize min-max normalization memory usage and time

  #68 opened 3 years ago by tacazares
  1

• Generate Data for Publication Figures

  #53 opened 3 years ago by tacazares
  0

• Write a maxATAC function to prepare ATAC-seq data from a BAM file and review main pipelines

  #67 opened 3 years ago by tacazares
  4

• Write a detailed prediction walkthrough

  #71 opened 3 years ago by tacazares
  2

• Integrate peak calling into prediction code

  #70 opened 3 years ago by tacazares
  0

• Preparing for the paper

  #61 opened 3 years ago by michael-kotliar
  1

• Installation errors when using Anaconda and maxATAC TensorFlow2.5

  #47 opened 3 years ago by tacazares
  1

• Remove maxATAC interpretation for independent development

  #59 opened 3 years ago by tacazares
  2

• Random Precision Benchmarking

  #49 opened 3 years ago by FaizRizvi
  1