NVIDIA-Genomics-Research AtacWorks issues

NVIDIA-Genomics-Research / AtacWorks

Deep learning based processing of Atac-seq data

https://clara-parabricks.github.io/AtacWorks/

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[sdk] create python package from AtacWorks src files

#102 tijyojwad closed 4 years ago
1
Issue with "--task regression" in main.py

#101 zchiang closed 4 years ago
4
Add unit tests for all modules

#100 ntadimeti closed 4 years ago
1
Interval reader

#99 avantikalal closed 4 years ago
2
main.py : Function to set random seed.

#98 ntadimeti closed 4 years ago
1
Add documentation for code

#97 ntadimeti closed 4 years ago
0
[dockerfile] Add dockerfile for AtacWorks repo

#96 tijyojwad closed 4 years ago
3
Reorganize main.py and other modules

#95 ntadimeti closed 4 years ago
1
Clean up main.py

#94 ntadimeti closed 4 years ago
1
[pip] fix numpy issue during requirements installation

#93 tijyojwad closed 4 years ago
0
[README] update readme.

#92 ntadimeti closed 4 years ago
1
[Readme] Explore options of testing the commands provided in Readme through CI.

#91 ntadimeti closed 4 years ago
1
Write detailed help for command line options in scripts.

#90 ntadimeti closed 4 years ago
1
Add config params config file

#89 ntadimeti closed 4 years ago
0
option to delete bedGraph file after inference

#88 avantikalal closed 4 years ago
0
Poissonloss

#87 avantikalal closed 4 years ago
1
[main] Fix API documentation

#86 tijyojwad closed 4 years ago
1
fixed bug in inference

#85 avantikalal closed 4 years ago
0
[main.py] Provide command line option for choosing best metric

#84 ntadimeti closed 4 years ago
2
Move model structure params into a file.

#83 ntadimeti closed 4 years ago
0
[main.py] Add a command line argument for rounding

#82 ntadimeti closed 4 years ago
0
fixed bug in AUC calculation

#81 avantikalal closed 4 years ago
0
[main] check dataset and interval size during inference

#80 tijyojwad closed 4 years ago
0
Changes to metrics calculation

#79 avantikalal closed 4 years ago
0
Spearman correlation calculation fails for large arrays (whole genome)

#78 avantikalal closed 4 years ago
0
Make rounding a command line argument

#77 avantikalal closed 4 years ago
1
option to supply separate peak file

#76 avantikalal closed 4 years ago
0
Merge master in dev-v0.2.0

#75 tijyojwad closed 4 years ago
0
[main] fix combining when some batches are skipped due to 0 value

#74 tijyojwad closed 4 years ago
0
Merge master into dev-v0.2.0

#73 tijyojwad closed 4 years ago
0
Pretrained cmd

#72 avantikalal closed 4 years ago
0
Merge dev-0.1.0 into master

#71 tijyojwad closed 4 years ago
0
[main.py] inference should terminate if `bedGraphToBigWig` throws an error

#70 avantikalal closed 4 years ago
0
[README] update README with cloning instructions

#69 tijyojwad closed 4 years ago
1
[main.py] Part-1/2, Do not pass args command into functions

#68 ntadimeti closed 4 years ago
1
Updated readme

#67 avantikalal closed 4 years ago
0
Alal/spearman

#66 avantikalal closed 4 years ago
0
[style] add linting to AtacWorks module

#65 tijyojwad closed 4 years ago
1
WIP: added quality metrics calculation

#64 avantikalal closed 4 years ago
2
WIP: additional metrics calculation for bigwig track quality

#63 avantikalal closed 4 years ago
0
[main.py] Add parallelization to writer

#62 ntadimeti closed 4 years ago
1
Add evaluation script for quality enhancement use case

#61 avantikalal opened 4 years ago
1
Alal/lognorm

#60 avantikalal closed 4 years ago
0
Testing log transformation of coverage tracks

#59 avantikalal closed 4 years ago
0
Benchmark end2end time with large dataset

#58 ntadimeti closed 4 years ago
2
[main.py] Add parallelization to writing out bedGraph files

#57 ntadimeti closed 4 years ago
3
Add Spearman Correlation to metrics and calculate_baseline_metrics.py

#56 avantikalal closed 4 years ago
0
choose metric for best model

#55 avantikalal closed 4 years ago
1
Organize main.py command line arguments into config file

#54 ntadimeti closed 4 years ago
3
Create a basic testing proposal

#53 ntadimeti closed 4 years ago
2

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