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microbiome
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mia
Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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loadFromMetaphlan: support taxonomy-named column
#499
TuomasBorman
closed
4 months ago
0
addHierarchyTree replaces existing tree
#498
TuomasBorman
opened
4 months ago
2
Error with loadFromMetaphlan
#497
J5886
closed
4 months ago
31
Deprecate taxonomyTree and addTaxonomyTree
#496
thpralas
closed
4 months ago
3
Fix splitOn bug
#495
thpralas
closed
4 months ago
0
splitOn adds rowTree instead of manipulating existing one
#494
thpralas
closed
2 months ago
2
agglomerateByRank fix: empty ranks
#493
TuomasBorman
closed
4 months ago
0
getPrevalence, named numeric(0) if NA values in the assay
#492
artur-sannikov
closed
4 months ago
0
readQZA fails
#491
antagomir
opened
4 months ago
3
Clarify pseudocount argument
#490
artur-sannikov
closed
4 months ago
0
Use `pseudocount=TRUE` in `transformAssay` even with missing or zero values
#489
artur-sannikov
opened
4 months ago
9
Clarify `pseudocounts` argument in `transformAssay`
#488
artur-sannikov
closed
3 months ago
2
agglomerateByRank: agglomerate tree fix
#487
TuomasBorman
closed
4 months ago
0
getPrevalence, NA values
#486
TuomasBorman
closed
4 months ago
4
loadFromMetaphlan: support for strain level
#485
TuomasBorman
closed
5 months ago
0
Getter and setters
#484
Daenarys8
closed
5 days ago
8
Getter and setters
#483
Daenarys8
closed
5 months ago
0
More layouts for plotAbundanceDensity
#481
artur-sannikov
opened
5 months ago
1
MARGIN and altexp parameters
#480
TuomasBorman
opened
6 months ago
1
New arguments for perSampleDominantFeatures
#479
himmil
closed
4 months ago
8
Fix critical issue with mergeFeatures
#478
Daenarys8
closed
1 month ago
13
cluster: fixes
#477
TuomasBorman
closed
4 months ago
1
taxonomyranks
#476
ake123
closed
4 months ago
8
#473
#475
himmil
closed
7 months ago
4
Function naming, logic, aliases
#474
TuomasBorman
opened
7 months ago
7
getExperimentCrossAssociation fails when sample names are missing
#473
antagomir
closed
7 months ago
8
Fix mergeSEs
#472
TuomasBorman
closed
8 months ago
0
Improved speed for loadHumann
#471
KatariinaParnanen
closed
8 months ago
0
Support for Metaphlan v2
#470
TuomasBorman
closed
8 months ago
0
Fix error, notes, and warning based on BiocCheck()
#469
erawijantari
closed
3 months ago
7
consider removing set.seed() inside the functions
#468
erawijantari
closed
7 months ago
2
transformAssay input
#467
antagomir
opened
8 months ago
0
Faith index fails
#466
antagomir
closed
7 months ago
6
Manpage clean-up
#465
jepasan
closed
8 months ago
1
Fix vignette
#464
TuomasBorman
closed
8 months ago
0
Rarified beta diversity calculations
#463
antagomir
opened
8 months ago
10
Unify parameter description
#462
Daenarys8
closed
5 days ago
5
runRDA fix, dissimilarity measure
#461
TuomasBorman
closed
8 months ago
0
estimateAlpha
#460
ChouaibB
closed
2 days ago
32
could not find function "DmmParam"
#459
AroArz
closed
9 months ago
2
Harmonizing documentation
#458
TuomasBorman
opened
9 months ago
1
Consider rworkflows
#457
TuomasBorman
closed
1 month ago
1
loadFromBiom fix
#456
TuomasBorman
closed
8 months ago
3
loadFromBiom fix
#455
TuomasBorman
closed
9 months ago
0
loadFromBiom fix
#454
TuomasBorman
closed
9 months ago
3
Export transformCounts
#453
TuomasBorman
closed
9 months ago
0
mergeSEs fix
#452
TuomasBorman
closed
8 months ago
0
Fix pseudocount bug for missing values in assay
#451
RiboRings
closed
9 months ago
0
Clean up the manpages
#450
antagomir
opened
9 months ago
3
Update transformAssay with pseudocount TRUE/FALSE option
#449
RiboRings
closed
9 months ago
1
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