Ecosyste.ms: Issues

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GitHub / BigDataBiology/argNorm issues and pull requests

#67 - DOC add link to funcscan

Pull Request - State: closed - Opened by Vedanth-Ramji about 1 month ago

#66 - Update docs for v0.6.0

Pull Request - State: closed - Opened by Vedanth-Ramji about 1 month ago

#64 - Update SARG db link in crude_db_harmonisation

Pull Request - State: closed - Opened by Vedanth-Ramji about 1 month ago

#63 - RFCT remove groot_ref_db parameter in map_to_aro

Pull Request - State: closed - Opened by Vedanth-Ramji about 2 months ago

#62 - ADD groot ARO mapping

Pull Request - State: closed - Opened by Vedanth-Ramji about 2 months ago

#61 - ADD raw & hamronized example groot outputs to test groot normalizer

Pull Request - State: closed - Opened by Vedanth-Ramji 2 months ago - 1 comment

#60 - ADD groot normalizer

Pull Request - State: closed - Opened by Vedanth-Ramji 2 months ago - 5 comments

#59 - Option to summarize multiple tool outputs into a single report

Issue - State: open - Opened by Matt-BF 2 months ago - 1 comment

#58 - DOC add nf-core module installation

Pull Request - State: closed - Opened by Vedanth-Ramji 3 months ago

#57 - ENH load CARD v3.2.9 when using RGI

Pull Request - State: closed - Opened by Vedanth-Ramji 3 months ago

#56 - ENH handle AROs as string rather than int in get_aro_mapping_table()

Pull Request - State: closed - Opened by Vedanth-Ramji 3 months ago - 2 comments

#55 - Updated manual curation for misannotated genes

Pull Request - State: closed - Opened by Vedanth-Ramji 3 months ago - 1 comment

#54 - ENH Update drug categorization logic

Pull Request - State: closed - Opened by Vedanth-Ramji 3 months ago

#53 - ADD use all parents for gene to drug mapping

Pull Request - State: closed - Opened by Vedanth-Ramji 3 months ago

#52 - BUG manually curate misannotated gene

Pull Request - State: closed - Opened by Vedanth-Ramji 3 months ago

#51 - ENH Update drug categorization logic

Pull Request - State: closed - Opened by Vedanth-Ramji 4 months ago

#50 - Remove duplicate mappings & sort megares_ARO_mapping

Pull Request - State: closed - Opened by Vedanth-Ramji 4 months ago - 1 comment

#48 - ADD missing ARO mappings to manual curation

Pull Request - State: closed - Opened by Vedanth-Ramji 4 months ago - 4 comments

#47 - DOC improve index.md

Pull Request - State: closed - Opened by Vedanth-Ramji 4 months ago

#45 - ENH Improve MEGARes Mappings

Pull Request - State: closed - Opened by Vedanth-Ramji 5 months ago

#44 - Update test_lib.py

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

#43 - Update cli.py

Pull Request - State: closed - Opened by sebastianLedzianowski 5 months ago - 3 comments

#41 - Update requirements.txt

Pull Request - State: closed - Opened by sebastianLedzianowski 5 months ago - 2 comments

#40 - argNorm should accept inputs in case-independent way (on command line)

Issue - State: closed - Opened by luispedro 5 months ago - 2 comments
Labels: enhancement, good first issue

#39 - DOC: Improve documentation for v0.3.0

Pull Request - State: closed - Opened by Vedanth-Ramji 5 months ago

#38 - ADD: cluster and reverse complement correction for resfinder

Pull Request - State: closed - Opened by Vedanth-Ramji 5 months ago - 3 comments

#37 - Document argannot amino acid file update in changelog

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago

#36 - ENH Get amino acid file for argannot rather than nucleotide file

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago - 3 comments

#34 - AttributeError: module 'collections' has no attribute 'Mapping'

Issue - State: open - Opened by VittoriaOssanna 6 months ago - 6 comments

#33 - ADD docs for conda installation

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago

#32 - ADD resfinderfg integrated with normalizers

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago

#31 - ENH Update argannot to V6

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago

#30 - BUG duplicated resfinder fixed

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago - 2 comments

#29 - DOC improve index.md

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago - 1 comment

#28 - ADD lib.py to make argnorm usable as a library

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago - 2 comments

#26 - DOC added argNorm workflow figure

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago - 2 comments

#25 - ADD Update documentation

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago

#23 - ENH Updated manual curation for latest RGI

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago - 1 comment

#22 - ENH Update pytest tests & add integration tests

Pull Request - State: closed - Opened by Vedanth-Ramji 6 months ago

#21 - Improved testing

Pull Request - State: closed - Opened by Vedanth-Ramji 7 months ago

#20 - Improved Testing

Pull Request - State: closed - Opened by Vedanth-Ramji 7 months ago

#19 - Correct mappings

Pull Request - State: closed - Opened by Vedanth-Ramji 7 months ago

#18 - Corrected mappings to match output of crude_db_harmonisation.py

Pull Request - State: closed - Opened by Vedanth-Ramji 7 months ago - 1 comment

#17 - Resfinderfg and sargfam update

Pull Request - State: closed - Opened by Vedanth-Ramji 7 months ago

#16 - Removed python syntax in output.

Pull Request - State: closed - Opened by Vedanth-Ramji 7 months ago

#15 - Added new column headings. Index removed in output

Pull Request - State: closed - Opened by Vedanth-Ramji 7 months ago

#14 - manual_curation data missing in pypi v0.1.0

Issue - State: closed - Opened by danielpodlesny 7 months ago - 1 comment

#13 - Update manual curation

Pull Request - State: closed - Opened by Vedanth-Ramji 8 months ago

#12 - Hamronized resfinderfg support and new outputs

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

#11 - Hamronized amrfinderplus support

Pull Request - State: closed - Opened by danielpodlesny 11 months ago - 1 comment

#10 - amrfinderplus support & conda installation

Issue - State: closed - Opened by JFsanchezherrero 11 months ago - 3 comments

#9 - Aro annot update

Pull Request - State: closed - Opened by Vedanth-Ramji 11 months ago - 1 comment

#8 - Drug Categorization Code Added

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

#7 - input for argNorm for ARGs-OAP

Issue - State: closed - Opened by ellyyuyang over 1 year ago - 1 comment

#6 - Refactor

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

#5 - Better tests

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

#4 - Better build

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

#3 - ENH reimplement argnorm with subclassing

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

#2 - BUG BLD Fix module name

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

#1 - Resfinderfg support

Issue - State: closed - Opened by AdeBC over 2 years ago - 1 comment
Labels: enhancement