Ecosyste.ms: Issues

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GitHub / kundajelab/bpnet issues and pull requests

#51 - modisco-run error

Issue - State: open - Opened by guandailu 4 months ago

#50 - Bump keras from 2.2.4 to 2.13.1

Pull Request - State: open - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#47 - DeepLIFT contribution scores for one-hot encoded nucleotides

Issue - State: closed - Opened by berkuva almost 2 years ago - 2 comments

#45 - Notebook not working

Issue - State: open - Opened by songzeji about 2 years ago - 2 comments

#44 - Error building Leidenalg wheel in Colab environment

Issue - State: open - Opened by cmboye over 2 years ago

#43 - running bpnet cwm-scan modisco

Issue - State: closed - Opened by kanglizhu over 2 years ago - 2 comments

#42 - preds.neg.bw and preds.pos.bw

Issue - State: closed - Opened by kanglizhu over 2 years ago

#41 - examples/recommendations for ATAC/Dnase-seq data

Issue - State: closed - Opened by ChangxuFan over 2 years ago - 4 comments

#40 - OverflowError: can't convert negative value to CHRPOS

Issue - State: closed - Opened by kanglizhu over 2 years ago

#39 - contrib.counts vs contrib.profile

Issue - State: closed - Opened by ChangxuFan over 2 years ago - 2 comments

#38 - Viewing the hypothetical impscores

Issue - State: open - Opened by evanseitz over 2 years ago - 2 comments

#37 - bpnet contrib function error

Issue - State: closed - Opened by Darlingfuer over 2 years ago

#36 - Removed multiprocessing during training

Pull Request - State: closed - Opened by albertjstanley almost 3 years ago - 1 comment

#35 - Error when traning ATAC-seq with one track

Issue - State: closed - Opened by zhenzuo2 almost 3 years ago

#34 - Removed multiprocessing during training

Pull Request - State: closed - Opened by albertjstanley about 3 years ago - 1 comment

#33 - Empty batch error loading training data into memory

Issue - State: open - Opened by drewjbeh about 3 years ago - 5 comments

#31 - bpnet installation problem

Issue - State: open - Opened by spour over 3 years ago - 1 comment

#30 - Have not tested but I belive I have code to exclude dna

Pull Request - State: closed - Opened by RachitSharma2001 over 3 years ago

#29 - installation problem

Issue - State: open - Opened by saralinker over 3 years ago

#28 - Fix: Added negative-strand, single-strand heatmap and bigwig features

Pull Request - State: closed - Opened by mlweilert over 3 years ago

#27 - examples file snakefile

Issue - State: closed - Opened by liameihao over 3 years ago - 1 comment

#26 - BED file with strands

Issue - State: closed - Opened by albertjstanley over 3 years ago - 2 comments

#25 - Normalizing by SeqLen in Profile Loss

Issue - State: closed - Opened by mhorlacher over 3 years ago - 2 comments

#24 - AttributeError: 'str' object has no attribute 'decode' error in bpnet contrib

Issue - State: closed - Opened by np519 over 3 years ago - 6 comments

#23 - pprint dependency prevents conda env create

Issue - State: open - Opened by kevbrick over 3 years ago - 8 comments

#22 - export-bw when training a model without negs errors out.

Issue - State: closed - Opened by snystrom over 3 years ago - 3 comments

#21 - current pysam version installs incorrect libssl

Issue - State: closed - Opened by snystrom over 3 years ago - 2 comments

#20 - "No object to concatenate" error

Issue - State: closed - Opened by eyalbenda over 3 years ago - 4 comments

#19 - Computation of hypothetical contributions

Issue - State: closed - Opened by Karollus almost 4 years ago - 3 comments

#18 - Run BPnet with one input bw track

Issue - State: open - Opened by yanwang271 almost 4 years ago - 4 comments

#17 - Remove pprint from setup.py

Pull Request - State: closed - Opened by an1lam about 4 years ago - 1 comment

#16 - `pip install bpnet` is broken due to `pprint` requirement

Issue - State: closed - Opened by an1lam about 4 years ago

#15 - Double-checking: full training data included in chip-nexus example?

Issue - State: open - Opened by an1lam over 4 years ago - 4 comments

#14 - Update README.md

Pull Request - State: closed - Opened by an1lam over 4 years ago - 1 comment

#13 - Cannot import name `AsyncKernelManager` in bpnet training step of Colab notebook

Issue - State: closed - Opened by an1lam over 4 years ago - 1 comment

#12 - Fix: Updated paths of get_ranges from ContribFile

Pull Request - State: closed - Opened by mlweilert over 4 years ago

#10 - Fix: .h5 contrib file now is compatible with ContribFile.get_profile()

Pull Request - State: closed - Opened by mlweilert almost 5 years ago

#9 - Fix: Contrib get_ranges .h5 parsing corrected.

Pull Request - State: closed - Opened by mlweilert almost 5 years ago

#8 - BPNet fails with wrong cudnn version, but tensorflow doesn't.

Issue - State: open - Opened by mmtrebuchet almost 5 years ago - 1 comment

#7 - Type error in modisco cwm-scan

Issue - State: closed - Opened by mmtrebuchet almost 5 years ago - 1 comment

#6 - bpnet export-bw skips contribution.bw file writing

Issue - State: closed - Opened by mlweilert about 5 years ago - 2 comments

#5 - subset bed file to bed3. add intervals_format arg

Pull Request - State: closed - Opened by Avsecz about 5 years ago

#4 - Datasets not loading correctly unless `--in-memory` specified.

Issue - State: closed - Opened by mlweilert about 5 years ago - 6 comments

#3 - Add an option to add track features to cwm-scan

Issue - State: open - Opened by Avsecz over 5 years ago

#2 - Cannot make documentation

Issue - State: open - Opened by mmtrebuchet over 5 years ago - 2 comments

#1 - input BED file needs to be BED3, not BED6

Issue - State: closed - Opened by mlweilert over 5 years ago - 1 comment