kipoi kipoiseq issues - Githubissues

kipoi / kipoiseq

Standard set of data-loaders for training and making predictions for DNA sequence-based models.

https://kipoi.org/kipoiseq/

MIT License

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issues

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U instead of STOP codon for TGA

#67 KalinNonchev closed 4 years ago
3
Protein dl grch38

#66 KalinNonchev closed 4 years ago
0
test optional dependencies

#65 MuhammedHasan opened 4 years ago
0
bug fix for typing

#64 MuhammedHasan closed 4 years ago
0
Add backwards compatibility; update PyRanges support

#63 Hoeze closed 4 years ago
0
add backwards compatibility

#62 Hoeze closed 4 years ago
0
Upgrade pyranges

#61 Hoeze closed 4 years ago
0
add some documentation

#60 Hoeze closed 4 years ago
3
protein dl

#59 MuhammedHasan closed 4 years ago
1
Drop python 3.5?

#58 Hoeze closed 4 years ago
3
Protein dl

#57 KalinNonchev closed 4 years ago
4
compare chroms, resolves #55

#56 MuhammedHasan opened 4 years ago
0
write function to check different chromosome annotations

#55 MuhammedHasan opened 4 years ago
0
get_variants implemented

#54 MuhammedHasan closed 4 years ago
0
implement `get_variant` for matching multiple variant

#53 MuhammedHasan closed 4 years ago
0
Fix doc for `extractors`

#52 MuhammedHasan opened 5 years ago
0
Variant matcher

#51 MuhammedHasan closed 5 years ago
1
queryable-vcf-files

#50 MuhammedHasan closed 5 years ago
1
migrate-extractor-to-kipoiseq-dataclasses

#49 MuhammedHasan closed 5 years ago
0
Remove label dtype/depend on BED row format

#48 stefanches7 opened 5 years ago
1
Update sequence.py

#47 stefanches7 opened 5 years ago
2
Add strand information to the sequence dataloaders

#46 stefanches7 opened 5 years ago
0
hotfix string formatting

#45 Avsecz closed 5 years ago
1
Added `kipoiseq.dataclasses.Variant` and `kipoiseq.dataclasses.Interval`

#44 Avsecz closed 5 years ago
0
queryable vcf file

#43 MuhammedHasan closed 5 years ago
2
version 0.2.5

#42 MuhammedHasan closed 5 years ago
0
changed ci script for build_deploy_docs target

#41 DerThorsten closed 5 years ago
0
Ci fixes

#40 DerThorsten closed 5 years ago
0
removed kipoi docker,use as many deps from conda as possible

#39 DerThorsten closed 5 years ago
0
changed ci

#38 DerThorsten closed 5 years ago
2
Update config.yml remove git-lfs install

#37 Avsecz opened 5 years ago
0
critical bug fix, insertion behavior changed

#36 MuhammedHasan closed 5 years ago
0
Implement filter method which allows user to write custom filters. Also implement common filters.

#35 MuhammedHasan closed 5 years ago
1
Allow multiple intervals as input

#34 MuhammedHasan closed 5 years ago
1
Split variant based on interval start-end if fixed_len, fixes #32

#33 MuhammedHasan closed 5 years ago
0
Split variant based on interval start-end if fixed_len=False

#32 MuhammedHasan closed 5 years ago
0
Validate reference sequence

#31 Avsecz closed 5 years ago
1
Implement `Variant` and `Interval` classes. Use them instead of `cyvcf2.Variant` and `pybedtools.Interval`

#30 Avsecz closed 5 years ago
2
In `SingleVariantVCFSeqExtractor` and `SingleSeqVCFSeqExtractor`, compare ref in vcf with fasta

#29 MuhammedHasan opened 5 years ago
0
Bug fixes for VCFSeqExtractor: #25 , #26 and compare ref with variant file.

#28 MuhammedHasan closed 5 years ago
0
Generate .fai file in the IntervalSeqDl __init__

#27 Avsecz opened 5 years ago
0
`SingleVariantVCFSeqExtractor` and `SingleSeqVCFSeqExtractor` assume 0-base vcf file

#26 MuhammedHasan closed 5 years ago
0
gt_types vs. genotypes-attribute for variant (extractor-MultiSampleVCF)

#25 JulianRein closed 5 years ago
1
Bump version: 0.2.2 → 0.2.3

#24 DerThorsten closed 5 years ago
0
Add vcf_seq extractor

#23 MuhammedHasan closed 5 years ago
1
Dependencies using kipoi-conda and kipoi-utils

#22 DerThorsten closed 5 years ago
0
Add dataloaders for variant-effect prediction

#21 Avsecz opened 5 years ago
0
remove h5py and related dependencies

#20 Avsecz closed 6 years ago
0
fix get_output_schema

#19 Avsecz closed 6 years ago
0
rename IntervalSeqDl -> SeqIntervalDl

#18 Avsecz closed 6 years ago
1

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