Changes in version 0.99.0 + Submitted to Bioconductor Changes in version 1.1.x + split transformCounts into transformSamples and transformFeatures + added log_modulo_skewness as a diversity index + added functions for summarizing dominant taxa information + added wrapper for adding dominant taxa information to colData + added specialized subsetting function for subsetting by prevalence (subsetByPrevalentTaxa/subsetByRareTaxa) + added mapTaxonomy + added estimateDivergence + bugfix: makePhyloseqFromTreeSummarizedExperiment checks now for rowTree be compatible + bugfix: meltAssay supports Matrix types + bugfix: meltAssay is able to include rowData also when there are duplicated rownames + added subsampleCounts for Subsampling/Rarefying data + added getExperimentCrossCorrelation for calculatting cross-correlation between features + added calculateOverlap + getUniqueTaxa & getTopTaxa: added option for alphabetical order Changes in version 1.3.x + name change: testForExperimentCrossCorrelation to testExperimentCrossCorrelation + getExperimentCrossCorrelation: Filtering disabled by default, option to suppress warnings + bugfix: taxonomyTree gave error if taxa were agglomerated at highest level (taxa name mismatch) + bugfix: subsampleCounts errors if no samples are found after subsampling + added loadFromMetaphlan + renamed calculateUniFrac to calculateUnifrac + added na.rm option to getTopTaxa function + bugfix: makeTreeSEFromPseq -- orientation of assay is taken into account + bugfix: getExperimentCrossCorrelation's "matrix"" mode works with features named equally + bugfix: getExperimentCrossCorrelation's calculates correlations correctly with features named equally + getExperimentCrossCorrelation name changed to getExperimentCrossAssociation + getExperimentCrossAssociation: user's own function supported, sort in mode == table enabled + getExperimentCrossAssociation: added MARGIN & paired options, efficiency of algorithm improved