Ecosyste.ms: Issues

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GitHub / sbslee/pypgx issues and pull requests

#142 - How PyPGx deal with missing data

Issue - State: open - Opened by xjq8065524 7 days ago - 2 comments

#141 - Working with Large BAM files

Issue - State: closed - Opened by abheda24 23 days ago - 8 comments

#140 - run-ngs-pipeline error with CYP2D6

Issue - State: closed - Opened by Cyaneiss about 1 month ago - 8 comments

#139 - Simplifying star allele calls to ignore Unknown Function

Issue - State: closed - Opened by toddknutson 3 months ago - 2 comments

#138 - AlleleNotFoundError: ('NAT2', '*12')

Issue - State: closed - Opened by toddknutson 3 months ago - 3 comments

#136 - UGT1A1 Structural variants

Issue - State: closed - Opened by Jorisvansteenbrugge 4 months ago - 2 comments

#135 - correct hg38 coordinate chr10:102830835 A>G

Pull Request - State: closed - Opened by NeiH4207 4 months ago - 2 comments

#134 - correct hg38 coordinate chr10:102830835 A>G

Pull Request - State: closed - Opened by NeiH4207 4 months ago - 2 comments

#133 - 0.25.0 dev

Pull Request - State: closed - Opened by sbslee 5 months ago

#132 - Using CRAM in stead of BAM files

Issue - State: open - Opened by ebernsen 5 months ago - 4 comments

#131 - v 0.24.0 copy-number-profile issue for G6PD and CYP2D6

Issue - State: closed - Opened by ChristineHOconnor 6 months ago - 2 comments

#130 - VCF contig error

Issue - State: closed - Opened by evyamor 6 months ago - 5 comments
Labels: bug

#128 - PYPGX workflow with premade VCF

Issue - State: closed - Opened by evyamor 7 months ago - 2 comments

#127 - Using bam files created with Illumina's graph reference as an input

Issue - State: closed - Opened by yaarau 7 months ago - 6 comments

#125 - 0.24.0 dev

Pull Request - State: closed - Opened by sbslee 8 months ago

#124 - Recommendations new version and custom recommendations

Issue - State: closed - Opened by Bioinf-usr 8 months ago - 2 comments

#122 - [Errno 95] Operation not supported

Issue - State: closed - Opened by Pharmacogenetecist 9 months ago - 1 comment

#121 - NumberFormatException in beagle

Issue - State: closed - Opened by leiste375 10 months ago - 4 comments

#120 - Long-Read Pipeline - unphased sites in VCF using WhatsHap

Issue - State: closed - Opened by sumudu-rangika 11 months ago - 9 comments

#119 - All G6PD phenotypes are "Indeterminate", even when it seems that some should not be based on the diplotype?

Issue - State: closed - Opened by brettva 11 months ago - 9 comments
Labels: enhancement

#118 - 0.23.0 dev

Pull Request - State: closed - Opened by sbslee 11 months ago

#117 - Major bug introduced in the 0.22.0 version

Issue - State: closed - Opened by sbslee 11 months ago
Labels: bug

#116 - 0.22.0 dev

Pull Request - State: closed - Opened by sbslee 12 months ago

#115 - MTHFR.vcf 1kgp pypgx bundle

Issue - State: closed - Opened by nbiesot 12 months ago - 12 comments
Labels: enhancement

#114 - Issue with pypgx.get_recommendation

Issue - State: closed - Opened by marcelthieljit about 1 year ago - 1 comment
Labels: bug

#113 - Beagle return non-zero exist status

Issue - State: closed - Opened by anh151 about 1 year ago - 3 comments
Labels: bug

#112 - scikit-learn version

Issue - State: closed - Opened by shimbalama about 1 year ago - 1 comment
Labels: duplicate

#111 - Data analysis

Pull Request - State: closed - Opened by shermcar about 1 year ago - 1 comment

#110 - Add files via upload

Pull Request - State: closed - Opened by shermcar about 1 year ago

#109 - Nanopore data

Issue - State: closed - Opened by kokyriakidis about 1 year ago

#108 - Issue with running a large sample dataset in pypgx

Issue - State: closed - Opened by sumudu-rangika about 1 year ago - 1 comment

#107 - Running the entire pipeline

Issue - State: closed - Opened by Sahana-selvarathnam about 1 year ago - 11 comments

#106 - estimate-phase-beagle can't open CYP2D6.vcf.gz

Issue - State: closed - Opened by NaphatCode about 1 year ago - 1 comment

#105 - Error finding file in ngs run

Issue - State: closed - Opened by muhligs about 1 year ago - 6 comments

#104 - Request - if possible - Allelic Depth

Issue - State: closed - Opened by Pharmacogenetecist about 1 year ago - 4 comments

#103 - SLCO1B1

Issue - State: closed - Opened by vaipathak about 1 year ago - 3 comments

#102 - 0.21.0 dev

Pull Request - State: closed - Opened by sbslee about 1 year ago

#101 - create-input-vcf error

Issue - State: closed - Opened by sharkLoc about 1 year ago - 13 comments

#100 - [Feature Request] Support custom location of pypgx-bundle files

Issue - State: closed - Opened by lexotero about 1 year ago - 8 comments
Labels: enhancement

#99 - CPIC level details

Issue - State: closed - Opened by hongsheng-lai over 1 year ago - 5 comments
Labels: enhancement

#98 - importing external CNV calls

Issue - State: closed - Opened by pjgreer over 1 year ago - 2 comments

#97 - Haplotypes called for IFNL3

Issue - State: closed - Opened by sumudu-rangika over 1 year ago - 3 comments
Labels: bug

#96 - ValueError: Different sample sets found in CLI but not API

Issue - State: closed - Opened by anh151 over 1 year ago - 10 comments
Labels: bug

#95 - Additional Pharmacogenes

Issue - State: closed - Opened by labdyn over 1 year ago - 2 comments

#94 - CYP2D6 *11 and *17

Issue - State: closed - Opened by brettva over 1 year ago - 2 comments

#93 - CYP2D6 *4 calls

Issue - State: closed - Opened by Pharmacogenetecist over 1 year ago - 6 comments

#92 - NGS pipeline error messages

Issue - State: closed - Opened by emeadd over 1 year ago - 1 comment
Labels: duplicate

#88 - Installation error?

Issue - State: closed - Opened by Pharmacogenetecist over 1 year ago - 10 comments
Labels: duplicate

#87 - BAM Identifiers/Filenames Are Alphanumeric Strings When Viewing Results

Issue - State: closed - Opened by erichards52 over 1 year ago - 3 comments

#86 - Recommendations for comparing pypgx calls to commercial tests?

Issue - State: closed - Opened by brettva almost 2 years ago - 6 comments

#84 - Is it possible to replace Depth of Coverage file with DP field?

Issue - State: closed - Opened by seokho92 almost 2 years ago - 2 comments

#83 - Interpreting Outputs

Issue - State: closed - Opened by anh151 almost 2 years ago - 4 comments

#82 - Minor bug in pipeline.py all functions

Issue - State: closed - Opened by anh151 almost 2 years ago - 3 comments

#81 - create-input-vcf error using numpy 1.24.1

Issue - State: closed - Opened by michela-marcellino almost 2 years ago - 1 comment

#79 - 0.20.0 dev

Pull Request - State: closed - Opened by sbslee almost 2 years ago

#77 - CPIC/PharamGKB recommendations

Issue - State: closed - Opened by Bioinf-usr almost 2 years ago - 4 comments

#76 - Segmentation fault when calling create_input_vcf through API or CLI

Issue - State: closed - Opened by sebapir about 2 years ago - 3 comments

#75 - Depth of coverage command.

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

#74 - Installation error

Issue - State: closed - Opened by Pharmacogenetecist about 2 years ago - 4 comments

#73 - Plotting allele fraction with empty VCF raises error

Issue - State: closed - Opened by sbslee about 2 years ago - 3 comments
Labels: bug

#72 - can CRAM be used as input?

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

#71 - 0.19.0 dev

Pull Request - State: closed - Opened by sbslee about 2 years ago

#69 - 0.18.0 dev

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

#68 - Issue while running snp chip tutorial.

Issue - State: closed - Opened by ngslearner over 2 years ago - 9 comments
Labels: bug

#67 - 0.17.0 dev

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

#66 - Why running my WGS data stops in the middle?

Issue - State: closed - Opened by sbargal1 over 2 years ago - 16 comments

#64 - Improve PyPGx's handling of genes on X chromosome (i.e. G6PD)

Issue - State: closed - Opened by sbslee over 2 years ago - 4 comments
Labels: enhancement

#63 - Beagle throws error when there is only one variant in input VCF

Issue - State: closed - Opened by sbslee over 2 years ago - 9 comments
Labels: bug

#62 - 0.16.0 dev

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

#61 - Error using bed

Issue - State: closed - Opened by Wilsonjsjunior over 2 years ago - 4 comments
Labels: bug

#60 - Error for pypgx installed by conda

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

#59 - Update CNV labels

Issue - State: closed - Opened by sbslee over 2 years ago
Labels: enhancement

#58 - 0.15.0 dev

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

#56 - Integration CNV/SV with PyPGx pipeline

Issue - State: closed - Opened by NTNguyen13 over 2 years ago - 4 comments

#55 - 0.14.0 dev

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

#54 - Introducing `create-input-vcf` command

Issue - State: closed - Opened by sbslee over 2 years ago
Labels: enhancement

#53 - CYP2B6*17 calling issue caused by having multiple variant synonyms

Issue - State: closed - Opened by sbslee over 2 years ago
Labels: enhancement

#52 - Impact of rs2032582A>C variant

Issue - State: closed - Opened by nmtrang00 over 2 years ago - 2 comments

#51 - Regarding RefAllele and Default Allele in gene-table.csv

Issue - State: closed - Opened by NTNguyen13 over 2 years ago - 4 comments

#50 - Update algorithm for whole gene duplication detection

Issue - State: closed - Opened by sbslee over 2 years ago
Labels: enhancement

#49 - Add the ABCG2 gene to PyPGx

Issue - State: closed - Opened by sbslee over 2 years ago - 5 comments
Labels: enhancement

#48 - 0.13.0 dev

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

#47 - 0.12.0 dev

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

#46 - CYP2B6 phenotyping/genotyping

Issue - State: closed - Opened by Pharmacogenetecist almost 3 years ago - 8 comments

#45 - Help with nanopore data

Issue - State: closed - Opened by Pharmacogenetecist almost 3 years ago - 6 comments
Labels: enhancement

#44 - Citing PyPGx

Issue - State: closed - Opened by NTNguyen13 almost 3 years ago - 5 comments

#43 - 0.11.0 dev

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

#42 - ImportError: cannot import name 'pycov' from 'fuc'

Issue - State: closed - Opened by geocarvalho almost 3 years ago - 2 comments

#41 - Fix major bug where CNV callers are not packaged properly

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

#40 - 0.10.0 dev

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

#39 - Update F5 gene to Pypgx

Pull Request - State: closed - Opened by NTNguyen13 almost 3 years ago - 2 comments

#38 - Update CFTR phenotype

Pull Request - State: closed - Opened by NTNguyen13 almost 3 years ago - 2 comments

#37 - Update phenotype for CFTR

Pull Request - State: closed - Opened by NTNguyen13 almost 3 years ago