Ecosyste.ms: Issues

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GitHub / kipoi/kipoiseq issues and pull requests

#117 - Bump tqdm from 4.45.0 to 4.66.3

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#116 - VariantSeqExtractor fix: allow padding if sequence gets out of bounds

Pull Request - State: closed - Opened by gtsitsiridis 9 months ago - 1 comment

#115 - fix "gt_type != 2" to 3 (unknown)

Pull Request - State: closed - Opened by shinichinamba about 2 years ago - 1 comment

#113 - Bump numpy from 1.18.3 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#112 - Allow to directly specify whether or not to use strand information

Pull Request - State: closed - Opened by Hoeze over 2 years ago

#111 - Listing dataloaders available

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

#110 - Pin sorted-nearest to 0.0.33

Pull Request - State: closed - Opened by haimasree over 2 years ago - 1 comment
Labels: bug

#109 - Pin sorted-nearest to 0.0.33

Issue - State: closed - Opened by haimasree over 2 years ago - 1 comment
Labels: bug

#108 - VCF_matching_bug_for_interval_arg, fixes #107

Pull Request - State: closed - Opened by MuhammedHasan almost 3 years ago

#107 - VCF matching returns false results when used with intervals argument

Issue - State: closed - Opened by MuhammedHasan almost 3 years ago
Labels: bug

#106 - "postprocessing" is this part of min_set_props?

Issue - State: open - Opened by MuhammedHasan almost 3 years ago
Labels: bug, question

#105 - fix variant end (#104)

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

#104 - Bug in variant end calculation

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

#103 - Fixing ci and moving pyranges to top level import

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

#102 - Error with AnchoredGTFDl

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

#101 - Kipoiseq installation problems

Issue - State: closed - Opened by PelFritz over 3 years ago

#100 - Allow to directly annotate a list of variants

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

#99 - Add one hot encode from enformer

Pull Request - State: closed - Opened by haimasree over 3 years ago - 2 comments

#98 - Remove default arguments from xpresso

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

#97 - Making info.authors a list

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

#96 - Kipoified xpresso dataloader

Pull Request - State: closed - Opened by haimasree over 3 years ago - 1 comment

#95 - pyranges import

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

#94 - variant combinator

Pull Request - State: closed - Opened by MuhammedHasan almost 4 years ago - 2 comments
Labels: enhancement

#93 - added anchoring

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

#92 - bug fix for split vcf file

Pull Request - State: closed - Opened by MuhammedHasan almost 4 years ago

#91 - Bug fix split vcf into chuncks

Pull Request - State: closed - Opened by MuhammedHasan almost 4 years ago

#90 - Api suggestion

Pull Request - State: open - Opened by Hoeze almost 4 years ago - 1 comment

#89 - Split vcf into chuncks

Pull Request - State: closed - Opened by MuhammedHasan almost 4 years ago - 1 comment

#88 - infer_from_cds in UTRFetcher does not work correctly

Issue - State: open - Opened by Hoeze almost 4 years ago - 1 comment

#87 - Resolve int conversion bug when inferring UTR from CDS

Pull Request - State: closed - Opened by Hoeze almost 4 years ago

#86 - Add automatic deployment

Pull Request - State: closed - Opened by Hoeze about 4 years ago

#85 - re-enabled use_strand option

Pull Request - State: closed - Opened by Karollus about 4 years ago

#84 - Updated UTR Fetcher and changed _filter_biotype and _filter_tag

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

#82 - Handle multi alternative variant in iteration

Pull Request - State: closed - Opened by MuhammedHasan over 4 years ago
Labels: enhancement

#81 - Implement inference for UTRFetcher

Issue - State: closed - Opened by Hoeze over 4 years ago

#80 - [WIP] UTR data loader

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

#78 - Phased dataloader

Issue - State: open - Opened by Hoeze over 4 years ago

#77 - make pyranges optional again

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

#76 - info about variants

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

#75 - dependabot

Pull Request - State: closed - Opened by KalinNonchev almost 5 years ago
Labels: enhancement

#74 - Extractors dataloader

Pull Request - State: closed - Opened by KalinNonchev almost 5 years ago - 1 comment
Labels: enhancement

#73 - Multiple variants

Pull Request - State: closed - Opened by KalinNonchev almost 5 years ago - 1 comment

#72 - bug with nan values in tag fixed for grch37

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

#71 - Vcf variants not defined

Pull Request - State: closed - Opened by KalinNonchev almost 5 years ago - 1 comment

#70 - vcf case for undefined variants - skip

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

#69 - Kalin nonchev protein dl grch38

Pull Request - State: closed - Opened by KalinNonchev almost 5 years ago - 2 comments

#68 - bug in second parameter `Interval` should be interval

Issue - State: open - Opened by MuhammedHasan almost 5 years ago
Labels: bug

#67 - U instead of STOP codon for TGA

Pull Request - State: closed - Opened by KalinNonchev almost 5 years ago - 3 comments

#66 - Protein dl grch38

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

#65 - test optional dependencies

Issue - State: open - Opened by MuhammedHasan almost 5 years ago
Labels: enhancement

#64 - bug fix for typing

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

#63 - Add backwards compatibility; update PyRanges support

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

#62 - add backwards compatibility

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

#61 - Upgrade pyranges

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

#60 - add some documentation

Pull Request - State: closed - Opened by Hoeze almost 5 years ago - 3 comments

#59 - protein dl

Pull Request - State: closed - Opened by MuhammedHasan about 5 years ago - 1 comment

#58 - Drop python 3.5?

Issue - State: closed - Opened by Hoeze about 5 years ago - 3 comments

#57 - Protein dl

Pull Request - State: closed - Opened by KalinNonchev about 5 years ago - 4 comments

#56 - compare chroms, resolves #55

Pull Request - State: open - Opened by MuhammedHasan about 5 years ago

#55 - write function to check different chromosome annotations

Issue - State: open - Opened by MuhammedHasan about 5 years ago
Labels: enhancement

#54 - get_variants implemented

Pull Request - State: closed - Opened by MuhammedHasan about 5 years ago
Labels: enhancement

#53 - implement `get_variant` for matching multiple variant

Issue - State: closed - Opened by MuhammedHasan about 5 years ago
Labels: enhancement

#52 - Fix doc for `extractors`

Issue - State: open - Opened by MuhammedHasan about 5 years ago
Labels: bug

#51 - Variant matcher

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago - 1 comment
Labels: enhancement

#50 - queryable-vcf-files

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago - 1 comment
Labels: enhancement

#49 - migrate-extractor-to-kipoiseq-dataclasses

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago
Labels: enhancement

#48 - Remove label dtype/depend on BED row format

Pull Request - State: open - Opened by stefanches7 over 5 years ago - 1 comment

#47 - Update sequence.py

Pull Request - State: open - Opened by stefanches7 over 5 years ago - 2 comments

#46 - Add strand information to the sequence dataloaders

Issue - State: open - Opened by stefanches7 over 5 years ago

#45 - hotfix string formatting

Pull Request - State: closed - Opened by Avsecz over 5 years ago - 1 comment

#44 - Added `kipoiseq.dataclasses.Variant` and `kipoiseq.dataclasses.Interval`

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

#43 - queryable vcf file

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago - 2 comments
Labels: enhancement

#42 - version 0.2.5

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago

#41 - changed ci script for build_deploy_docs target

Pull Request - State: closed - Opened by DerThorsten over 5 years ago

#40 - Ci fixes

Pull Request - State: closed - Opened by DerThorsten over 5 years ago

#39 - removed kipoi docker,use as many deps from conda as possible

Pull Request - State: closed - Opened by DerThorsten over 5 years ago

#38 - changed ci

Pull Request - State: closed - Opened by DerThorsten over 5 years ago - 2 comments

#37 - Update config.yml remove git-lfs install

Pull Request - State: open - Opened by Avsecz over 5 years ago

#36 - critical bug fix, insertion behavior changed

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago
Labels: bug

#35 - Implement filter method which allows user to write custom filters. Also implement common filters.

Issue - State: closed - Opened by MuhammedHasan over 5 years ago - 1 comment
Labels: enhancement

#34 - Allow multiple intervals as input

Issue - State: closed - Opened by MuhammedHasan over 5 years ago - 1 comment
Labels: enhancement

#33 - Split variant based on interval start-end if fixed_len, fixes #32

Pull Request - State: closed - Opened by MuhammedHasan over 5 years ago
Labels: bug

#32 - Split variant based on interval start-end if fixed_len=False

Issue - State: closed - Opened by MuhammedHasan over 5 years ago
Labels: bug

#31 - Validate reference sequence

Issue - State: closed - Opened by Avsecz almost 6 years ago - 1 comment
Labels: duplicate

#30 - Implement `Variant` and `Interval` classes. Use them instead of `cyvcf2.Variant` and `pybedtools.Interval`

Issue - State: closed - Opened by Avsecz almost 6 years ago - 2 comments
Labels: enhancement

#28 - Bug fixes for VCFSeqExtractor: #25 , #26 and compare ref with variant file.

Pull Request - State: closed - Opened by MuhammedHasan almost 6 years ago
Labels: bug

#27 - Generate .fai file in the IntervalSeqDl __init__

Issue - State: open - Opened by Avsecz almost 6 years ago

#25 - gt_types vs. genotypes-attribute for variant (extractor-MultiSampleVCF)

Issue - State: closed - Opened by JulianRein almost 6 years ago - 1 comment
Labels: bug

#24 - Bump version: 0.2.2 → 0.2.3

Pull Request - State: closed - Opened by DerThorsten almost 6 years ago

#23 - Add vcf_seq extractor

Pull Request - State: closed - Opened by MuhammedHasan almost 6 years ago - 1 comment
Labels: enhancement

#22 - Dependencies using kipoi-conda and kipoi-utils

Pull Request - State: closed - Opened by DerThorsten almost 6 years ago

#21 - Add dataloaders for variant-effect prediction

Issue - State: open - Opened by Avsecz about 6 years ago

#20 - remove h5py and related dependencies

Pull Request - State: closed - Opened by Avsecz about 6 years ago

#18 - rename IntervalSeqDl -> SeqIntervalDl

Pull Request - State: closed - Opened by Avsecz about 6 years ago - 1 comment

#17 - Rename dataloaders and reordered shape

Pull Request - State: closed - Opened by Avsecz about 6 years ago - 2 comments