BigDataBiology argNorm issues

BigDataBiology / argNorm

ARG normalization by mapping to the ARO ontology.

MIT License

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issues

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DOC add link to funcscan

#67 Vedanth-Ramji closed 1 week ago
0
Update docs for v0.6.0

#66 Vedanth-Ramji closed 2 weeks ago
0
ADD code to give percentages & frequencies of perfect, strict, and loose hits

#65 Vedanth-Ramji closed 2 weeks ago
0
Update SARG db link in crude_db_harmonisation

#64 Vedanth-Ramji closed 2 weeks ago
0
RFCT remove groot_ref_db parameter in map_to_aro

#63 Vedanth-Ramji closed 3 weeks ago
0
ADD groot ARO mapping

#62 Vedanth-Ramji closed 1 month ago
0
ADD raw & hamronized example groot outputs to test groot normalizer

#61 Vedanth-Ramji closed 1 month ago
1
ADD groot normalizer

#60 Vedanth-Ramji closed 3 weeks ago
5
Option to summarize multiple tool outputs into a single report

#59 Matt-BF opened 1 month ago
1
DOC add nf-core module installation

#58 Vedanth-Ramji closed 2 months ago
0
ENH load CARD v3.2.9 when using RGI

#57 Vedanth-Ramji closed 3 weeks ago
0
ENH handle AROs as string rather than int in get_aro_mapping_table()

#56 Vedanth-Ramji closed 2 months ago
2
Updated manual curation for misannotated genes

#55 Vedanth-Ramji closed 2 months ago
1
ENH Update drug categorization logic

#54 Vedanth-Ramji closed 2 months ago
0
ADD use all parents for gene to drug mapping

#53 Vedanth-Ramji closed 2 months ago
0
BUG manually curate misannotated gene

#52 Vedanth-Ramji closed 2 months ago
0
ENH Update drug categorization logic

#51 Vedanth-Ramji closed 2 months ago
0
Remove duplicate mappings & sort megares_ARO_mapping

#50 Vedanth-Ramji closed 2 months ago
1
DOC Update changelog with adding missing manual curtion & case-independent inputs on command-line

#49 Vedanth-Ramji closed 3 months ago
0
ADD missing ARO mappings to manual curation

#48 Vedanth-Ramji closed 3 months ago
4
DOC improve index.md

#47 Vedanth-Ramji closed 3 months ago
0
ENH specific version for NCBI in db_harmonisation & clean up harmonisation code

#46 Vedanth-Ramji closed 3 months ago
0
ENH Improve MEGARes Mappings

#45 Vedanth-Ramji closed 3 months ago
0
Update test_lib.py

#44 sebastianLedzianowski closed 3 months ago
0
Update cli.py

#43 sebastianLedzianowski closed 3 months ago
3
ENH handle mapping not in ARO in map_to_aro function & simplify map_to_aro() code

#42 Vedanth-Ramji closed 4 months ago
0
Update requirements.txt

#41 sebastianLedzianowski closed 4 months ago
2
argNorm should accept inputs in case-independent way (on command line)

#40 luispedro closed 2 months ago
2
DOC: Improve documentation for v0.3.0

#39 Vedanth-Ramji closed 4 months ago
0
ADD: cluster and reverse complement correction for resfinder

#38 Vedanth-Ramji closed 4 months ago
3
Document argannot amino acid file update in changelog

#37 Vedanth-Ramji closed 4 months ago
0
ENH Get amino acid file for argannot rather than nucleotide file

#36 Vedanth-Ramji closed 4 months ago
3
ENH update conda install command to make sure conda-forge is used

#35 Vedanth-Ramji closed 5 months ago
0
AttributeError: module 'collections' has no attribute 'Mapping'

#34 VittoriaOssanna opened 5 months ago
6
ADD docs for conda installation

#33 Vedanth-Ramji closed 5 months ago
0
ADD resfinderfg integrated with normalizers

#32 Vedanth-Ramji closed 5 months ago
0
ENH Update argannot to V6

#31 Vedanth-Ramji closed 5 months ago
0
BUG duplicated resfinder fixed

#30 Vedanth-Ramji closed 5 months ago
2
DOC improve index.md

#29 Vedanth-Ramji closed 3 months ago
1
ADD lib.py to make argnorm usable as a library

#28 Vedanth-Ramji closed 4 months ago
2
ENH Remove warnings, add db validation for AbricateNormalizer, add file being normalized in CLI msg.

#27 Vedanth-Ramji closed 5 months ago
0
DOC added argNorm workflow figure

#26 Vedanth-Ramji closed 5 months ago
2
ADD Update documentation

#25 Vedanth-Ramji closed 5 months ago
0
ENH Update drug categorization to use drug categories of superclasses.

#24 Vedanth-Ramji closed 5 months ago
0
ENH Updated manual curation for latest RGI

#23 Vedanth-Ramji closed 5 months ago
1
ENH Update pytest tests & add integration tests

#22 Vedanth-Ramji closed 5 months ago
0
Improved testing

#21 Vedanth-Ramji closed 5 months ago
0
Improved Testing

#20 Vedanth-Ramji closed 5 months ago
0
Correct mappings

#19 Vedanth-Ramji closed 5 months ago
0
Corrected mappings to match output of crude_db_harmonisation.py

#18 Vedanth-Ramji closed 5 months ago
1