kundajelab bpnet issues

kundajelab / bpnet

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

http://bit.ly/bpnet-colab

MIT License

142 stars 35 forks source link

issues

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modisco-run error

#51 guandailu opened 3 months ago
0
Bump keras from 2.2.4 to 2.13.1

#50 dependabot[bot] opened 3 months ago
0
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 2 years ago
0
Notebook not working

#45 songzeji opened 2 years 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 3 years ago
1
Empty batch error loading training data into memory

#33 drewjbeh opened 3 years ago
5
Bpnet Added Channels Leads to Profile Predictions of 0

#32 RachitSharma2001 opened 3 years ago
0
bpnet installation problem

#31 spour opened 3 years ago
1
Have not tested but I belive I have code to exclude dna

#30 RachitSharma2001 closed 3 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 4 years ago
1
`pip install bpnet` is broken due to `pprint` requirement

#16 an1lam closed 4 years ago
0
Double-checking: full training data included in chip-nexus example?

#15 an1lam opened 4 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 5 years ago
2
subset bed file to bed3. add intervals_format arg

#5 Avsecz closed 5 years ago
0
Datasets not loading correctly unless `--in-memory` specified.

#4 mlweilert closed 5 years ago
6
Add an option to add track features to cwm-scan

#3 Avsecz opened 5 years ago
0
Cannot make documentation

#2 mmtrebuchet opened 5 years ago
2