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kundajelab
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bpnet
Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
http://bit.ly/bpnet-colab
MIT License
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ERROR: No matching distribution found for deepexplain (Installation of BPnet)
#49
genecell
opened
1 year ago
0
what is the expected input and targets for BPnet profile prediction
#48
PelFritz
closed
1 year ago
0
DeepLIFT contribution scores for one-hot encoded nucleotides
#47
berkuva
closed
1 year ago
2
Installation error, likely crashing due to dependency DeepExplain
#46
mauliknariya
opened
1 year ago
0
Notebook not working
#45
songzeji
opened
1 year ago
2
Error building Leidenalg wheel in Colab environment
#44
cmboye
opened
2 years ago
0
running bpnet cwm-scan modisco
#43
kanglizhu
closed
2 years ago
2
preds.neg.bw and preds.pos.bw
#42
kanglizhu
closed
2 years ago
0
examples/recommendations for ATAC/Dnase-seq data
#41
ChangxuFan
closed
1 year ago
4
OverflowError: can't convert negative value to CHRPOS
#40
kanglizhu
closed
2 years ago
0
contrib.counts vs contrib.profile
#39
ChangxuFan
closed
2 years ago
2
Viewing the hypothetical impscores
#38
evanseitz
opened
2 years ago
2
bpnet contrib function error
#37
Darlingfuer
closed
2 years ago
0
Removed multiprocessing during training
#36
albertjstanley
closed
2 years ago
1
Error when traning ATAC-seq with one track
#35
zhenzuo2
closed
2 years ago
0
Removed multiprocessing during training
#34
albertjstanley
closed
2 years ago
1
Empty batch error loading training data into memory
#33
drewjbeh
opened
2 years ago
5
Bpnet Added Channels Leads to Profile Predictions of 0
#32
RachitSharma2001
opened
2 years ago
0
bpnet installation problem
#31
spour
opened
2 years ago
1
Have not tested but I belive I have code to exclude dna
#30
RachitSharma2001
closed
2 years ago
0
installation problem
#29
saralinker
opened
3 years ago
0
Fix: Added negative-strand, single-strand heatmap and bigwig features
#28
mlweilert
closed
3 years ago
0
examples file snakefile
#27
liameihao
closed
3 years ago
1
BED file with strands
#26
albertjstanley
closed
3 years ago
2
Normalizing by SeqLen in Profile Loss
#25
mhorlacher
closed
3 years ago
2
AttributeError: 'str' object has no attribute 'decode' error in bpnet contrib
#24
np519
closed
3 years ago
6
pprint dependency prevents conda env create
#23
kevbrick
opened
3 years ago
8
export-bw when training a model without negs errors out.
#22
snystrom
closed
3 years ago
3
current pysam version installs incorrect libssl
#21
snystrom
closed
3 years ago
2
"No object to concatenate" error
#20
eyalbenda
closed
3 years ago
4
Computation of hypothetical contributions
#19
Karollus
closed
3 years ago
3
Run BPnet with one input bw track
#18
yanwang271
opened
3 years ago
4
Remove pprint from setup.py
#17
an1lam
closed
3 years ago
1
`pip install bpnet` is broken due to `pprint` requirement
#16
an1lam
closed
3 years ago
0
Double-checking: full training data included in chip-nexus example?
#15
an1lam
opened
3 years ago
4
Update README.md
#14
an1lam
closed
4 years ago
1
Cannot import name `AsyncKernelManager` in bpnet training step of Colab notebook
#13
an1lam
closed
4 years ago
1
Fix: Updated paths of get_ranges from ContribFile
#12
mlweilert
closed
4 years ago
0
Revert "Fix: .h5 contrib file now is compatible with ContribFile.get_profile()"
#11
mlweilert
closed
4 years ago
0
Fix: .h5 contrib file now is compatible with ContribFile.get_profile()
#10
mlweilert
closed
4 years ago
0
Fix: Contrib get_ranges .h5 parsing corrected.
#9
mlweilert
closed
4 years ago
0
BPNet fails with wrong cudnn version, but tensorflow doesn't.
#8
mmtrebuchet
opened
4 years ago
1
Type error in modisco cwm-scan
#7
mmtrebuchet
closed
4 years ago
1
bpnet export-bw skips contribution.bw file writing
#6
mlweilert
closed
4 years ago
2
subset bed file to bed3. add intervals_format arg
#5
Avsecz
closed
4 years ago
0
Datasets not loading correctly unless `--in-memory` specified.
#4
mlweilert
closed
4 years ago
6
Add an option to add track features to cwm-scan
#3
Avsecz
opened
4 years ago
0
Cannot make documentation
#2
mmtrebuchet
opened
4 years ago
2
input BED file needs to be BED3, not BED6
#1
mlweilert
closed
4 years ago
1