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ondevel

Commits on Nov 5, 2026
- Calculate dissimilarity matrix with getDissimilarity inside getPERMANOVA (#886)
  TuomasBorman
  authored
  b5aacf7
- Revise applyByModule (#883)
  
  authored
  2a0b4f4
Commits on Oct 30, 2026
- Align method = 'log' with log2 and log10 in transformAssay (#813) (#848)
  
  0xMuluh
  and
  TuomasBorman
  authored
  bf0da35
Commits on Oct 29, 2026
- Fix addQC docs (#881)
  TuomasBorman
  authored
  b04e8bd
Commits on Oct 28, 2026
- Initialise exporters to raw, qiime and mothur (#823)
  
  authored
  532d4b9
- Add cv to getQC (#875)
  TuomasBorman
  authored
  cd81123
- Document Joint-RPCA filtering examples (#842)
  
  authored
  d1f6f38
- Rename getQCMetrics and addQCMetrics to getQC and addQC (#868)
  
  0xMuluh
  and
  TuomasBorman
  authored
  5474afd
Commits on Oct 27, 2026
- Add getPCA and addPCA (#870)
  
  0xMuluh
  and
  TuomasBorman
  authored
  a15be3f
- Default getMDS and addMDS to no feature filtering (ntop = Inf) (#794)
  
  authored
  01119c3
- Warn instead of failing when overwriting assays (#873)
  
  0xMuluh
  and
  TuomasBorman
  authored
  9d5eb16
- Add sd and cv methods to getTop (#863)
  
  0xMuluh
  and
  TuomasBorman
  authored
  4bd520f
- Fix Camargo evenness computed on wrong entries (#866)
  
  authored
  9161756
Commits on Oct 26, 2026
- Add getDysbiosis and addDysbiosis (#862)
  
  0xMuluh
  and
  TuomasBorman
  authored
  d241b00
- Add getQCMetrics and addQCMetrics (#861)
  
  0xMuluh
  and
  TuomasBorman
  authored
  77707c0
Commits on Oct 22, 2026
- Add Allen's phylogenetic entropy and Rao's quadratic entropy to addAlpha (#845) (#847)
  
  0xMuluh
  and
  TuomasBorman
  authored
  b3ac981
Commits on Oct 20, 2026
- Fix/optimize multiple alpha index rarefaction (#857)
  
  raivo-otus
  and
  TuomasBorman
  authored
  d4884e7
Commits on Oct 2, 2026
- Initialise applyByModule (#825)
  
  Giulio Benedetti
  and
  TuomasBorman
  authored
  b78e622
Commits on Sep 25, 2026
- Support UniFrac and pre-calculated dissimilarity in getPERMANOVA (#844) (#846)
  
  0xMuluh
  and
  TuomasBorman
  authored
  2cba739
Commits on Sep 24, 2026
- Add rank support to getTop (#799)
  
  0xMuluh
  and
  TuomasBorman
  authored
  e425d95
- Update documents and namespace
  TuomasBorman
  committed
  416de1c
Commits on Sep 23, 2026
- Add Rdpack references (#797)
  
  0xMuluh
  and
  TuomasBorman
  authored
  751d24e
Commits on Jul 30, 2026
- Filter RPCAInput (#837)
  
  sabujcb
  and
  TuomasBorman
  authored
  b7072b9
Commits on Jun 16, 2026
- Fix joint rpca handling (#831)
  
  sabujcb
  and
  TuomasBorman
  authored
  8246e29
Commits on May 31, 2026
- Generalise agglomerateByModule to non-binary numerical modules (#824)
  
  Giulio Benedetti
  and
  TuomasBorman
  authored
  ded155a
Commits on Apr 17, 2026
- Patch: Shift to mia version of scuttle function to aggregate rows by group (#820)
  
  Giulio Benedetti
  and
  TuomasBorman
  authored
  f81d66a
Commits on Mar 23, 2026
- Extended author info for JointRPCA (#811)
  antagomir
  authored
  3dd0ded
Commits on Mar 16, 2026
- Improve Joint-RPCA (#808)
  
  TuomasBorman
  and
  0xMuluh
  authored
  abff00d
Commits on Mar 6, 2026
- Add support for ordination results in clustering (#809)
  TuomasBorman
  authored
  e9190ad
Commits on Feb 25, 2026
- Add Joint-RPCA to mia: methods, tests (#804)
  
  authored
  8157c60
Commits on Feb 23, 2026
- Feat/binning transformation (#801)
  
  raivo-otus
  and
  TuomasBorman
  authored
  915e796
Commits on Dec 9, 2025
- Change unifrac implementation from rbiom to ecodive (#786)
  
  authored
  3645a0c
Commits on Dec 8, 2025
- Fix typos in documentation for Double Principal Correspondence analysis: "Correspondance" → "Correspondence" (#792)
  
  hindrek
  and
  TuomasBorman
  committed
  26eec84
- update mia_logo (#784)
  
  0xMuluh
  authored and
  TuomasBorman
  committed
  ffc3129
Commits on Sep 10, 2025
- Add inverse rank normalisation (invnorm) to transformAssay (#766)
  
  eotamm
  and
  TuomasBorman
  authored
  48e3197

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Commits on Sep 10, 2025