kipoi kipoi-veff issues

kipoi / kipoi-veff

Variant effect prediction plugin for Kipoi

https://kipoi.org/veff-docs

MIT License

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issues

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How can I use the "ax=None" in the plot_mutmap function?

#46 robertzeibich opened 2 years ago
0
Getting a NotImplementedError: "sortBed" does not appear to be installed or on the path... error when running score_variants

#45 sukritikumar4 opened 2 years ago
1
compatability issues with installation of deepsea

#44 cmlakhan opened 3 years ago
1
Fix a bug when ALT is empty

#43 s6juncheng opened 3 years ago
0
Update dev-requirements-py36.yml - freeze pandas version

#42 Avsecz closed 4 years ago
0
Update mutators.py

#41 Avsecz opened 4 years ago
0
Simple change to make tqdm progress more notebook friendly

#40 gokceneraslan closed 4 years ago
0
Typo fix for the error message in score.py

#39 gokceneraslan closed 4 years ago
1
Results differ unexpectedly between `pipeline.predict` and `query_bed` with `ref` score

#38 an1lam opened 4 years ago
6
Update .circleci/config.yml

#37 Avsecz closed 4 years ago
5
Fix `MutationMap.query_bed`

#36 an1lam closed 4 years ago
9
Fix typo in mutation map instructions

#35 an1lam closed 4 years ago
1
dataloader_args

#34 ggabernet closed 5 years ago
2
Bump version: 0.2.3 → 0.3.0

#33 DerThorsten closed 5 years ago
0
Niceparse

#32 DerThorsten closed 5 years ago
0
Bump version: 0.2.2 → 0.2.3

#31 DerThorsten closed 5 years ago
0
Dependencies: Using kipoi_utils

#30 DerThorsten closed 5 years ago
0
fix None handling for ID=.

#29 dansimancas closed 5 years ago
0
Update setup.py

#28 Avsecz closed 5 years ago
0
Speedup writing to file

#27 Avsecz opened 5 years ago
1
added --singularity to score_variants

#26 Avsecz closed 5 years ago
0
options to show ref_seq, box ref allele

#25 s6juncheng closed 5 years ago
0
fix logging

#24 krrome closed 5 years ago
1
Kipoi-veff fails silently when the input files don't exist

#23 Avsecz closed 5 years ago
2
Add logit_diff scoring function.

#22 Avsecz opened 5 years ago
0
Write buffer

#21 Avsecz closed 5 years ago
1
Error when chromosome names don't start with `chr`

#20 Avsecz opened 5 years ago
1
batch-writing to the vcf file

#19 Avsecz closed 5 years ago
1
No error message if the input file doesn't exist

#18 dansimancas closed 5 years ago
1
Use HDF5BatchWriter instead of deepdish when writing the results for hdf5 files

#17 Avsecz opened 5 years ago
0
Comply with dl repo

#16 krrome closed 5 years ago
0
Comply with dl repo + allow bed row index as variant index

#15 krrome closed 5 years ago
2
update ModelInfoExtractor

#14 krrome closed 5 years ago
1
updated docs

#13 Avsecz closed 6 years ago
1
Docs improvement

#12 Avsecz opened 6 years ago
0
create tempfile. closes #10

#11 Avsecz closed 6 years ago
1
Make a duplicate of variants.vcf when testing

#10 krrome closed 6 years ago
2
restrict version to kipoi >=0.4

#9 Avsecz opened 6 years ago
0
allow `stdout` filename on score_variants

#8 Avsecz opened 6 years ago
0
Migrate all `kipoi.postprocessing.variant_effects` to `kipoi_veff`

#7 Avsecz closed 6 years ago
1
indel support: predict_mutations_on_batch()

#6 krrome opened 6 years ago
0
indel support: dataloader-utility:VcfReader

#5 krrome opened 6 years ago
0
indel support overview

#4 krrome opened 6 years ago
0
indel support: dataloader-utility: MutationDatasetMixin

#3 krrome opened 6 years ago
0
indel support: dataloader-utility: VariantSeqExtractor

#2 krrome opened 6 years ago
0
Implementation timeline

#1 krrome opened 6 years ago
0