microbiome/mia

Issues

• dbRDA and loadings

  #634 opened 4 months ago by TuomasBorman
  1

• RDA speedup

  #633 opened 4 months ago by antagomir
  0

• Remove authors from functions

  #628 opened 5 months ago by TuomasBorman
  1

• mia::importHUMAnN() problem

  #627 opened 5 months ago by antagomir
  0

• more functional importers (e.g. humann)

  #622 opened 5 months ago by antagomir
  2

• Harmonizing documentation

  #458 opened 5 months ago by TuomasBorman
  3

• addDivergence from OMA vignette

  #624 opened 5 months ago by shwetha141
  17

• Use vegan in rarefy

  #561 opened 7 months ago by TuomasBorman
  16

• Add (optionally) information on butyrate producers to rowData in importing the taxonomic abundances

  #621 opened 5 months ago by antagomir
  0

• Use `pseudocount=TRUE` in `transformAssay` even with missing or zero values

  #489 opened 5 months ago by artur-sannikov
  13

• plotRDA feature loadings

  #604 opened 6 months ago by antagomir
  4

• Compute and plot feature loadings in ordination methods

  #596 opened 5 months ago by thpralas
  7

• Get top explanatory features from PCoA loadings

  #541 opened 5 months ago by RiboRings
  10

• agglomerate by rank duplicated taxa names

  #617 opened 5 months ago by li-fangyeo
  13

• Error with loadFromMetaphlan

  #497 opened 10 months ago by J5886
  34

• Update contributors list

  #601 opened 5 months ago by TuomasBorman
  6

• More layouts for plotAbundanceDensity

  #481 opened 5 months ago by artur-sannikov
  3

• readQZA fails

  #491 opened a year ago by antagomir
  4

• MARGIN and altexp parameters

  #480 opened 5 months ago by TuomasBorman
  1

• Improve documentation

  #585 opened 5 months ago by TuomasBorman
  12

• Unclear matrix row after agglomerateByRank

  #559 opened 5 months ago by maartenciers
  8

• get vs. add

  #535 opened 5 months ago by antagomir
  2

• transformAssay input

  #467 opened a year ago by antagomir
  1

• R CMD Check contains NOTES

  #532 opened 8 months ago by TuomasBorman
  3

• addHierarchyTree replaces existing tree

  #498 opened 5 months ago by TuomasBorman
  4

• Error length.out in subsampleCounts()

  #560 opened 6 months ago by imonteroo
  3

• Adding CSS to transformAssay() function

  #610 opened 6 months ago by SHillman836
  12

• Error using mia::transformCounts

  #565 opened 6 months ago by CecileBlanchon
  4

• convertToBIOM

  #605 opened 6 months ago by TuomasBorman
  0

• prevalence functions and as_relative parameter

  #577 opened 6 months ago by TuomasBorman
  0

• Rename MARGIN

  #578 opened 6 months ago by TuomasBorman
  1

• mergeSEs: tree merging

  #558 opened 6 months ago by TuomasBorman
  2

• Merging trees

  #569 opened 6 months ago by TuomasBorman
  1

• agglomerateByPrevalence does not return rowTree

  #573 opened 6 months ago by thpralas
  1

• Detection vs prevalence improve documentation

  #580 opened 6 months ago by artur-sannikov
  1

• z transformation naming to change

  #583 opened 7 months ago by antagomir
  4

• Faith index

  #522 opened 9 months ago by antagomir
  0

• remove_empty_ranks in agglomerateByRanks

  #568 opened 7 months ago by TuomasBorman
  0

• pseudocount

  #564 opened 7 months ago by TuomasBorman
  0

• splitOn adds rowTree instead of manipulating existing one

  #494 opened 8 months ago by thpralas
  2

• Fix estimateDiversity input check

  #519 opened 8 months ago by TuomasBorman
  0

• Rarified beta diversity calculations

  #463 opened a year ago by antagomir
  10

• Support for Qiime2R

  #512 opened 9 months ago by antagomir
  3

• Clarify `pseudocounts` argument in `transformAssay`

  #488 opened 9 months ago by artur-sannikov
  2

• getPrevalence, named numeric(0) if NA values in the assay

  #492 opened 10 months ago by artur-sannikov
  0

• Function naming, logic, aliases

  #474 opened a year ago by TuomasBorman
  7

• Faith index fails

  #466 opened a year ago by antagomir
  6

• consider removing set.seed() inside the functions

  #468 opened a year ago by erawijantari
  2

• getExperimentCrossAssociation fails when sample names are missing

  #473 opened a year ago by antagomir
  8

• could not find function "DmmParam"

  #459 opened a year ago by AroArz
  2