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calico
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basenji
Sequential regulatory activity predictions with deep convolutional neural networks.
Apache License 2.0
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failed running "basenji_sat_bed.py" in tutorials
#152
yal054
closed
1 year ago
4
train/test/valid sequences for predetermined regions
#151
icdh99
closed
1 year ago
2
fasta file of saluki_predict_fasta.py
#150
Jojo-LIU-LIU
closed
1 year ago
1
Can I apply Basenji's series of functions to the Enformer model?
#149
zhanxiangzong
closed
1 year ago
2
"When the bin size needs to be adjusted (e.g. from 128 to 100), how should I design the optimal pooling kernel size?"
#148
zhanxiangzong
closed
1 year ago
2
No checkpoints found.
#147
wittney-m
opened
1 year ago
3
is it still unfinished?
#146
latortseva
opened
1 year ago
1
akita_data_read.py % string make target to zero
#145
r1cheu
closed
1 year ago
3
Error when running akita_train.py
#144
fokxon
opened
1 year ago
9
cooler file preprocessing for Akita
#143
pjlaw
closed
1 year ago
1
Memory requirements for tfr_hdf5.py on basenji_human tfrecords
#142
rnsherpa
closed
2 years ago
2
tutorial broke
#141
mepster
closed
1 year ago
1
Nan values during training
#140
tfabiha
opened
2 years ago
1
I can't get data from this given url
#139
HandsomeLuoyang
closed
2 years ago
1
Error in running basenji_data.py
#138
luohaitaofujian
opened
2 years ago
1
What was the hardware setup used to train the best models for Basenji?
#137
sheetalgiri
opened
2 years ago
1
Basset style predictions - parameter tuning.
#136
gouthamatla
opened
2 years ago
4
Test gene expression predictions link is broken
#135
obada-alzoubi
closed
2 years ago
1
Error in running basenji_data.py
#134
luohaitaofujian
opened
2 years ago
1
how to download the cross2020 model and data?
#133
lancezhangsf
opened
2 years ago
11
How to preprocess bed file from ReMap for training
#132
songzeji
opened
2 years ago
2
Cannot Download from Basenji Google Cloud
#131
EricZQu
closed
2 years ago
2
basenji_data.py does not produce tfr files and have no error message
#130
songzeji
closed
2 years ago
0
Suggestion for tutorial notebooks (preprocessing)
#129
a1ultima
opened
2 years ago
5
Clarifications about unmappable genomic regions
#128
GrossTor
opened
2 years ago
7
Akita CTCF perturbation
#127
shtoneyan
opened
2 years ago
4
Hard coded conda prefix
#126
SuhasSrinivasan
closed
2 years ago
2
Using dataset.apply with drop_remainder=True
#125
maldil
closed
2 years ago
1
Mouse Cell Atlas reads are aligned to mm9 whereas basenji predicts from mm10
#124
GrossTor
closed
2 years ago
2
Load Akita TFRecords Data
#123
stasys-hub
opened
2 years ago
2
Akita: result has no change after I deleted some sequences
#122
gxygogogo
opened
2 years ago
1
norm the effect size across chromosomes
#121
yinhongwei4079
opened
2 years ago
1
The trouble when using explore_model.ipynb of Akita
#120
gxygogogo
closed
2 years ago
1
option-for-verbose=False-in-json
#119
gfudenberg
closed
2 years ago
1
"RuntimeWarning: divide by zero encountered in log" in akita_data_read.py
#118
BatyrM
opened
2 years ago
1
prespecified.yml outdated
#117
z2e2
closed
2 years ago
1
use basenji to motif discovery - motif scanning
#116
moxgreen
opened
2 years ago
2
ValueError in restoring model for akita
#115
j3gu
closed
2 years ago
2
Alignment of CAGE-seq reads
#114
GrossTor
opened
2 years ago
5
Getting NAs while trying to compute Variant effect predictions using basenji_sad.py
#113
sukritikumar4
opened
2 years ago
5
Reproducing Saluki
#112
cwadaniels7
closed
2 years ago
5
Pass the loss label, not loss function, as an argument
#111
damkokot
closed
2 years ago
1
How are TSSs extracted from GENCODE files?
#110
cristianregep
opened
2 years ago
1
Basset-style training failing due to shape mismatch
#109
twrightsman
opened
2 years ago
6
Question - Akita Test Set Loss Replication
#108
GreatArcStudios
closed
2 years ago
11
How to reproduce Supplementary_Figure_S9and apply it to other dataset
#107
Licko0909
opened
2 years ago
5
Testing Basset-style Basenji
#106
htdashti
closed
2 years ago
4
basenji_data.py error
#105
beoungl
opened
2 years ago
3
Target Description
#104
khoangothe
closed
2 years ago
2
Clarifying data processing pipeline
#103
adazhang1
closed
3 years ago
2
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