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MiraldiLab
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maxATAC
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Apache License 2.0
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Final modifications pre-publication submission
#81
tacazares
closed
2 years ago
1
Finalize Code Base
#80
FaizRizvi
closed
1 year ago
14
Refactor
#79
FaizRizvi
closed
2 years ago
0
Refactor threshold
#78
FaizRizvi
closed
2 years ago
0
Update peak centric prediction
#77
tacazares
closed
1 year ago
0
Refactor par pred
#76
FaizRizvi
closed
2 years ago
1
Refactor prepare
#75
tacazares
closed
2 years ago
0
Refactor variant predict
#74
tacazares
closed
2 years ago
0
Refactor peaks
#73
FaizRizvi
closed
2 years ago
0
Refactor peaks
#72
tacazares
closed
2 years ago
0
Write a detailed prediction walkthrough
#71
tacazares
closed
2 years ago
2
Integrate peak calling into prediction code
#70
tacazares
closed
2 years ago
0
Optimize whole-genome prediction time
#69
tacazares
closed
2 years ago
1
Optimize min-max normalization memory usage and time
#68
tacazares
closed
2 years ago
1
Write a maxATAC function to prepare ATAC-seq data from a BAM file and review main pipelines
#67
tacazares
closed
2 years ago
4
Implement and document a way to retrieve the required reference data
#66
tacazares
closed
2 years ago
3
Docker and install
#65
FaizRizvi
closed
2 years ago
16
Define the list of the commands a user will be able to run and what results they will produce
#64
michael-kotliar
closed
2 years ago
1
Make sure the maxATAC python package can be installed on python 3.7/3.8/3.9 on both Ubuntu and macOS
#63
michael-kotliar
closed
1 year ago
5
Refactor. Work in progress
#62
michael-kotliar
closed
2 years ago
9
Preparing for the paper
#61
michael-kotliar
closed
2 years ago
1
Develop is59
#60
tacazares
closed
2 years ago
0
Remove maxATAC interpretation for independent development
#59
tacazares
closed
2 years ago
2
Numpy compatibility for Tensorflow 2.5 and SHAP in interpreting analysis jobs
#58
XiaotingChen
opened
3 years ago
2
Develop is54
#57
tacazares
closed
3 years ago
0
OSC Node Crash invoked by Kernel Bug
#56
FaizRizvi
closed
2 years ago
1
Develop
#55
FaizRizvi
closed
3 years ago
0
Error in how area under the precision recall curve is calculated
#54
tacazares
closed
2 years ago
0
Generate Data for Publication Figures
#53
tacazares
closed
2 years ago
0
Develop cheers
#52
FaizRizvi
closed
3 years ago
0
Develop cheers
#51
FaizRizvi
closed
3 years ago
0
Develop
#50
tacazares
closed
3 years ago
0
Random Precision Benchmarking
#49
FaizRizvi
closed
3 years ago
1
Develop is46
#48
tacazares
closed
3 years ago
0
Installation errors when using Anaconda and maxATAC TensorFlow2.5
#47
tacazares
closed
2 years ago
1
Invalid Interval Bounds Error When Training
#46
tacazares
closed
3 years ago
0
Reverse_complement training flag
#45
FaizRizvi
closed
3 years ago
2
Develop normalize
#44
tacazares
closed
3 years ago
0
Update average documentation + default chroms are autosomal
#43
tacazares
closed
3 years ago
0
Finalize maxATAC v1 ATAC-seq data
#42
tacazares
closed
3 years ago
2
Issue with Loading Models during Prediction. Clash between keras and tensorflow.keras
#41
dlab-arp
closed
3 years ago
1
Issue with plotting models. Potential clash between keras and tf.keras modules
#40
dlab-arp
closed
3 years ago
1
Develop is30 strand tf2
#39
FaizRizvi
closed
3 years ago
1
epoch_selection changes
#38
FaizRizvi
closed
3 years ago
0
Develop IS30 stranded prediction
#37
tacazares
closed
3 years ago
0
Develop is30 strand
#36
tacazares
closed
3 years ago
0
Epoch Selection: Performance using chr 2 Training Cell Line AUPR vs Performance using Validation Dice Coefficient
#35
FaizRizvi
closed
3 years ago
0
Stranded Prediction Benchmarking
#34
FaizRizvi
closed
3 years ago
0
maxATAC install issues on local machines
#33
FaizRizvi
closed
3 years ago
7
Test bowtie2 alignment vs STAR
#32
tacazares
closed
3 years ago
1
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