MiraldiLab maxATAC issues

MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

Apache License 2.0

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issues

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add thread option to prediction

#131 XiaotingChen opened 3 months ago
0
Change Path for

#130 Elfaba opened 4 months ago
1
import error _OrderedEnqueuer_ tensorflow.keras.utils

#129 martinezvbs opened 4 months ago
6
Error on running prepare: subprocess.CalledProcessError

#128 Lozzard closed 7 months ago
1
Update prediction_tools.py

#127 ANRudrapatna closed 7 months ago
0
pseudo-bulk

#126 drosop closed 9 months ago
3
Fixing ModuleNotFoundError: No module named 'keras.utils.data_utils'

#125 XiaotingChen closed 9 months ago
0
Update predict.md

#124 ANRudrapatna closed 7 months ago
2
Update train.md

#123 ANRudrapatna closed 7 months ago
0
keras error after installation

#122 sleepryansleep closed 9 months ago
2
Update normalize.md

#121 ANRudrapatna closed 3 months ago
2
Update predict.md

#120 ANRudrapatna opened 1 year ago
0
`maxATAC` prepare with sc 10X ATAC

#119 daccachejoe opened 1 year ago
2
Update DEFAULT_BENCHMARKING_BIN_SIZE to align with publication

#118 XiaotingChen closed 1 year ago
0
pyBigWig values method does not take argument numpy=True

#117 tanjimin opened 1 year ago
1
Question about training/testing celltypes

#116 ninashenker closed 1 year ago
1
Error on running predict: could not load dynamic library for tensorflow

#115 timothykoala opened 1 year ago
1
Error on running prepare function - error while loading shared libraries: libncurses.so.5

#114 timothykoala closed 1 year ago
2
Publication updates

#113 tacazares closed 1 year ago
0
Remove hardcoded paths in `maxatac prepare` and in maxatac_data so users can provide custom chromosome sets

#112 tacazares closed 1 year ago
6
What is the fourth column in the bed file the variants function produce?

#111 songzeji closed 1 year ago
2
Mm

#110 FaizRizvi closed 1 year ago
1
Fix flags across functions for consistency

#109 tacazares closed 1 year ago
0
Add code for plots/update functions associated with `normalize`, `average`, `prepare`, and `benchmark`

#108 tacazares opened 2 years ago
0
Improve `maxatac prepare`

#107 tacazares closed 1 year ago
1
Multiprocessing with Ordered Enquerer

#106 FaizRizvi closed 2 years ago
1
101 roi generator, documentation, and get_target_matrix function added

#105 tacazares closed 2 years ago
0
Add tests and set up some Continuous Integration (CI)

#104 tacazares opened 2 years ago
0
Documentation Updates

#103 tacazares closed 2 years ago
0
bedGraphToBigWig: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

#102 tacazares closed 1 year ago
1
Update `maxatac train` and optimize

#101 tacazares closed 2 years ago
1
Graphviz error with `maxatac train`

#100 tacazares closed 2 years ago
0
#97 Update prepare function for scATAC-seq

#99 tacazares closed 2 years ago
0
93 variants parser

#98 tacazares closed 2 years ago
0
`maxatac prepare` issue processing scATAC-seq fragment files

#97 tacazares closed 2 years ago
0
`maxatac prepare` erroring out at normalization

#96 codymowery closed 2 years ago
2
#93 fix missing chrom_sizes for ROI based variant predictions

#95 FaizRizvi closed 2 years ago
0
#93 fix variants.py and associated parser in parser.py

#94 tacazares closed 2 years ago
0
variants_bed invalid int value

#93 hrayjones closed 1 year ago
13
Best value to use for thresholds

#91 tacazares closed 1 year ago
1
Interesting observation with predictions: Blacklist update

#90 tacazares closed 2 years ago
2
train.md clarifications

#89 emiraldi closed 2 years ago
0
docs/readme/peaks.md disconnect example / arguments

#88 emiraldi closed 2 years ago
1
Installation issues with pyBigWig not finding numpy

#87 tacazares closed 2 years ago
0
--agg options for benchmark.md

#86 emiraldi closed 2 years ago
2
default for noramlize.md

#85 emiraldi closed 2 years ago
0
Benchmarking: separate quantitative and binary evaluation

#84 emiraldi closed 2 years ago
0
Enhancements: sex chromosome predictions

#83 emiraldi closed 2 years ago
2
Build AppImage for Linux

#82 michael-kotliar closed 2 years ago
3
Final modifications pre-publication submission

#81 tacazares closed 2 years ago
1