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taxprofiler
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taxpasta
TAXnomic Profile Aggregation and STAndardisation
https://taxpasta.readthedocs.io/
Apache License 2.0
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WIP: fix links by using relative ones to markdown files
#103
Midnighter
closed
1 year ago
5
Avoid type coercion for domain models
#102
Midnighter
opened
1 year ago
0
feat: raise parser warning as exception
#101
Midnighter
closed
1 year ago
2
[BUG] Certain parser problems are only warnings
#100
Midnighter
closed
1 year ago
0
Address #98.
#99
jfy133
closed
1 year ago
2
[BUG] Improve docs on tutorial data & warning against cross-profile merging
#98
jfy133
closed
1 year ago
0
Add curl commands to quickly fetch example files
#97
Midnighter
closed
1 year ago
2
docs: improve description of options behavior
#96
Midnighter
closed
1 year ago
1
Split up getting started to simplified version and deep dive
#95
jfy133
closed
1 year ago
1
[BUG] Getting started tutorial is too complex
#94
jfy133
closed
1 year ago
0
Document that setting the output format overrules any given file extension
#93
Midnighter
closed
1 year ago
0
Document a curl command to download sample files in the readme
#92
Midnighter
closed
1 year ago
0
Add repostatus.org badge
#91
Midnighter
closed
1 year ago
1
Add repostatus.org badge
#90
Midnighter
closed
1 year ago
0
Fix all links
#89
jfy133
closed
1 year ago
1
[BUG] Some internal links on readthedeocs broken
#88
jfy133
closed
1 year ago
0
[BUG] taxpasta deletes nodes/names.dmp from --taxonomy dir
#87
kdm9
closed
1 year ago
5
Insert taxonomic information in a more suitable column order
#86
Midnighter
closed
1 year ago
1
Fix metaphlan tax ID being -1 and combine all unclassified counts
#85
Midnighter
closed
1 year ago
1
refactor: generally allow 1% tolerance of compositionality
#84
Midnighter
closed
1 year ago
2
Issue regarding Taxpasta application in the kaiju classification tables.[BUG]
#83
LilyAnderssonLee
closed
1 year ago
6
Metaphlan3 output contains reads classified as taxid '-1' [BUG]
#82
prototaxites
closed
1 year ago
2
[Feature] Reorder columns after merging when options "--add-name/rank/lineage" and wide format are selected
#81
alexhbnr
closed
1 year ago
0
Render without rich
#80
Midnighter
closed
1 year ago
0
Documentation: minor typo fixes and phrasing tweaks
#79
jfy133
closed
1 year ago
2
Note on terminology and background
#78
Midnighter
closed
1 year ago
1
Post-tutorial cleanup
#77
Midnighter
closed
1 year ago
0
fix: increase the tolerance when comparing floats
#76
Midnighter
closed
1 year ago
1
[BUG] Bracken compositionality tolerance is too strict
#75
Midnighter
closed
1 year ago
0
fix: correctly set the version according to hatch-vcs
#74
Midnighter
closed
1 year ago
1
[Feature] Allow to set threshold for compositionality check of Bracken results
#73
alexhbnr
closed
5 months ago
13
[BUG] inconsistency formatting behaviour between standardise and merge
#72
jfy133
opened
1 year ago
4
Delete tutorial.qmd
#71
jfy133
closed
1 year ago
1
Document optional dependencies
#70
Midnighter
closed
1 year ago
4
Document extras in installation docs
#69
Midnighter
closed
1 year ago
0
Add the Zenodo webhook and badge
#68
Midnighter
closed
1 year ago
1
fix: provide files directly to `TaxDb`
#67
Midnighter
closed
1 year ago
0
Add longer/detailed Tutorial
#66
jfy133
closed
1 year ago
2
Expand installation and contribution docs
#65
Midnighter
closed
1 year ago
1
docs: expand about section and add to main readme
#64
Midnighter
closed
1 year ago
1
Update installation tools and configuration
#63
Midnighter
closed
1 year ago
1
Fix GH workflow
#62
Midnighter
closed
1 year ago
0
Fix: handle metaphlan profiles with unclassified taxa in the lineage
#61
Midnighter
closed
1 year ago
3
Feat taxonomy
#60
Midnighter
closed
1 year ago
0
Add taxonomy to BIOM format
#59
Midnighter
closed
1 year ago
1
Fix bug in krakenuniq
#58
sofstam
closed
1 year ago
1
Variability in KrakenUniq output causes bugs
#57
jfy133
closed
1 year ago
0
Document which column used in standarised profiles
#56
jfy133
closed
1 year ago
1
Correct document where the supported kaiju file comes from
#55
jfy133
closed
1 year ago
1
Kaiju documentation specifies incorrect input source
#54
jfy133
closed
1 year ago
0
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