Changes in version 1.21 o Fixed explained percentages on PCA axes for jointRPCA and hardened rank-deficient SVD handling in joint-RPCA (1.21.1, 2026-05-12) * Generalise agglomerateByModule to non-binary numerical modules (1.21.2, 2026-05-31) Changes in version 1.19 o Fixed a bug related to agglomerateByPrevalence and referenceSeq agglomeration (2025-12-08) o Use ecodive in UniFrac (1.19.2, 2025-12-09) o Added binning transformation (1.19.3, 2026-02-23) o Added support for reducedDim in clustering (1.19.5, 2026-03-06) Changes in version 1.17 o Added add.dimred parameter to meltSE() (2025-04-29) o Added transformation method that replaces values <= threshold with NA (2025-05-09) o importMetaPhlAn: Preserve features without taxonomy o Added agglomerateByModule() o Added inverse rank normalization (2025-09-10) Changes in version 1.15 o subsetBy*: added update.tree argument o agglomerateBy*: Add na.rm option for excluding NA counts o Added getPERMANOVA and addPERMANOVA functions to calculate PERMANOVA o update.tree = TRUE by default o Add functions for classifying taxa based on their average abundance o Add addPrevalence function that adds results of getPrevalence to rowData o Added support for dimred to getCrossAssociation o Add wrapper for PhILR transformation o Support rarefaction when applying unifrac o Added getMDS and addMDS: wrappers for scater::calculateMDS and scater::runMDS o Fix tree merging and agglomeration o getReducedDimAttribute: function for fetching elements from attributes of reducedDim o Improve decontam functions o Support precalculated dissimilarity matrix in dbRDA o Calculate standard, binary Jaccard index by default Changes in version 1.13 o Added new functions getMediation and addMediation o replace getExperiment* and testExperiment* functions with getCrossAssociation o Replace mergeRows and mergeCols with new function agglomerateByVariable o agglomerateByRank: bugfix related to agglomeration of non-existing tree o getHierarchyTree: bugfix related to empty cells in rowData o agglomerateByRank: bugfix: trees was not pruned correctly o rename meltAssay to meltSE o Rename countDominantFeatures and countDominantTaxa to summarizeDominance o rename subsetByPrevalent* and subsetByRare* to subsetByPrevalent and subsetByRare o Deprecate transformFeatures, transformSamples, transformCounts, Ztransform, relAbundanceCounts o rename getRare* functions to getRare, getUnique* functions to getUnique, getTop* functions to getTop and getPrevalent* functions to getPrevalent o Rename subsampleCounts to rarefyAssay o Rename perSampleDominant* functions to getDominant and addPerSampleDominant* functions to addDominant o Rename splitByRanks to agglomerateByRanks and add option as.list o Explain that rarefyAssay returns a new SummarizedExperiment object that includes the newly added subsampled assay. o Fix bug in mergeFeaturesByPrevalence o new aliases calculateDPCoA to getDPCoA, calculateNMDS to getNMDS, calculateRDA to getRDA, calculateCCA to getCCA o add informative error message in rarefyAssay on assays with strictly-negative values o Use rbiom package in unifrac implementation o Updated parameter names to follow naming convention "parameter.name" o rename converters makeTreeSEFrom* to convertFrom* and makePhyloseqFromTreeSE to convertToPhyloseq o add rowTree agglomeration and RefSeq agglomeration in agglomerateByPrevalence o Fix tree merging in unsplit and mergeSEs functions o Added addAlpha; a wrapper for calculating all alpha diversity indices o Added importTaxpasta o Changes in default taxonomy ranks; more ranks supported o Added Tito2024QMP dataset o Added convertToBIOM o new methods getLDA and addLDA for LDA ordination with feature loadings computation o new methods getNMF and addNMF for NMF ordination with feature loadings computation o If missing values, give informative error in *RDA/*CCA functions o transformAssay can apply transformation to altExp o Added CSS transformation o In agglomerateByVariable, splitOn and getDominant, use 'group' to specify grouping variable. Changes in version 1.11 o loadFromMetaphlan: support strain rank o agglomerateByRank: agglomerate tree fix o Replace taxonomyTree and addTaxonomyTree with getHierarchyTree and addHierarchyTree o splitOn: update rowTree fix o perSampleDominantFeatures: add new arguments (n, other.name, complete) o loadFromMetaphlan: support "taxonomy" column for specifying taxonomy o cluster: Overwrite old results instead of failing o getPrevalence: bugfix, if assay contains NA values, it does not end up to NA anymore. o getExperimentCrossCorrelation fix: enable using of sampleMap in MAE. o Implemented the setTaxonomyRanks function to specify which ranks are recognized as taxonomy ranks. o Rename cluster to addCluster o rename importers loadFromBiom, loadFromQIIME2, readQZA, loadFromMothur, loadFromMetaphlan, loadFromHumann o fix typo in loadFromBiom definition (deprecate file) o deprecate subsetSamples, subsetFeatures and subsetTaxa o deprecate plotNMDS after moving it to miaViz o rename estimateDivergence to addDivergence o Add details to documentation of function agglomerateByPrevalence Changes in version 1.9 o loadFromMetaphlan: Bugfix, not all files include ID column. o cluster: added wrapper for bluster's clusterRows function o Added loadFromHumann o calculateDMM: deprecated/updated outdated functions o Added Tengeler2020 dataset o *RDA & *CCA: calculate also statistical significance o altExp support for meltAssay o Deprecate mergeRows, mergeCols, agglomerateByRank, agglomerateByPrevalence o Removed getAbundanceSample and getAbundanceFeature o Updated test to avoid warning from deprecated functions o Export mergeFeaturesByRank o *RDA & *CCA: scores parameter for specifying output o Improve mergeSEs and loadFromBiom o Faith index: bugfix o runRDA bugfix: vegan::dbrda and vegan::vegdist have different parameter for dissimilarity --> taken into account o Add support for Metaphlan v2 o loadFromHumann: Improved speed Changes in version 1.7 o Deprecated assay_name arguments, replaced with assay.type o Removed abund_values argument o makePhyloseqFromTreeSE: added option for choosing a tree from multiple rowTrees o mergeSEs: match rows based on all available taxonomy level data on rowData o mergeSEs: fix bug related to equally named variables that are different class o mergeSEs: option for merging multiple assays o calculateUnifrac: option for specifying the tree from TreeSE o transformAssay: utilize vegan package o calculateUnifrac: subset tree based on data o agglomerateByRank: take into account multiple trees o loadFromBiom: name columns of rowData based on prefixes o Deprecate transformSamples, *Features, relabundance, ZTransform, relAbundanceCounts o mergeSEs: faster tree merging o Faith's index: fix bug that occurred when only one taxon is present Changes in version 1.5 o Added HintikkaXOData o Added sample metadata option to getExperimentCrossAssociation o estimateFaith: add support for multiple rowTrees o calculateRDA/CCA: added variable argument & replaced altexp argument with altExp o getExpCrossCorr: bugfix; samples should match when correlations between features are calculated o getExpCrossCorr: Kendall's tau is the default method o mergeSEs: bugfix; links between trees and rows/cols were wrong & rowData did not include all info o calculateDPCoA, calculateUnifrac & merge: add support for multiple trees o altExp parameter to altexp o agglomerateByRank: make rownames unique by default o removed calculateDistance and calculateUniFrac alias o calculateUnifrac bugfix Changes in version 1.3 o name change: testForExperimentCrossCorrelation to testExperimentCrossCorrelation o getExperimentCrossCorrelation: Filtering disabled by default, option to suppress warnings o bugfix: taxonomyTree gave error if taxa were agglomerated at highest level (taxa name mismatch) o bugfix: subsampleCounts errors if no samples are found after subsampling o added loadFromMetaphlan o renamed calculateUniFrac to calculateUnifrac o added na.rm option to getTopTaxa function o bugfix: makeTreeSEFromPseq -- orientation of assay is taken into account o bugfix: getExperimentCrossCorrelation's "matrix"" mode works with features named equally o bugfix: getExperimentCrossCorrelation's calculates correlations correctly with features named equally o getExperimentCrossCorrelation name changed to getExperimentCrossAssociation o getExperimentCrossAssociation: user's own function supported, sort in mode == table enabled o getExperimentCrossAssociation: added MARGIN & paired options, efficiency of algorithm improved o Added *Features aliases for *Taxa functions o *RDA functions utilize vegan:dbrda instead of vegan:rda o Sped up estimateDivergence by removing unnecessary pairwise comparisons o Added new internal function .calculate_reference_distance to calculate distance to a single reference sample o added new skin microbiome example data set 'peerj13075' o added splitOn and unsplitOn functions o CLR transformation: remove internal relative transformation o Replace 'abund_values' argument with 'assay_name' o getExpCrossCorr: added altExp option o added detection threshold option to getTopTaxa o makeSummarizedExperimentFromBiom is now makeTreeSummarizedExperimentFromBiom o Added mergeSE function o bugfix: loadFromBiom Changes in version 1.1 o split transformAssay into transformSamples and transformFeatures o added log_modulo_skewness as a diversity index o added functions for summarizing dominant taxa information o added wrapper for adding dominant taxa information to colData o added specialized subsetting function for subsetting by prevalence (subsetByPrevalentTaxa/subsetByRareTaxa) o added mapTaxonomy o added estimateDivergence o bugfix: makePhyloseqFromTreeSummarizedExperiment checks now for rowTree be compatible o bugfix: meltAssay supports Matrix types o bugfix: meltAssay is able to include rowData also when there are duplicated rownames o added subsampleCounts for Subsampling/Rarefying data o added getExperimentCrossCorrelation for calculatting cross-correlation between features o added calculateOverlap o getUniqueTaxa & getTopTaxa: added option for alphabetical order Changes in version 0.99.0 o Submitted to Bioconductor