NEWS.md

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

biomeUtils 0.022

• Remove clusterASVs function, changes to DECIPHER led to failure.

biomeUtils 0.020

• Remove cloudStatistic function.
• Remove dysbiosisScore function.
• Fix getSampleTibble function when SampleID is present in sample_data().

biomeUtils 0.020

• Added cloudStatistic function.

biomeUtils 0.019

• Added getYCTheta function.
• Fixed typo dysbiosisScore function.

biomeUtils 0.018

• Added dysbiosisScore function.

biomeUtils 0.017

• Fixed check errors.
• Added uniqueness function.
• Fixed bug in checkPolyphyletic.

biomeUtils 0.016

• Added filterTaxaTotal functions.
• Added transformation functions.

biomeUtils 0.015

• Added chekFilterEffect functions.

biomeUtils 0.014

• Added readMergedMetaphlan.

biomeUtils 0.013

• Added genericUtilities.
• Added saveData.

biomeUtils 0.012

• Added pullPhyloseq.
• Added separateSampleColumn.
• Added uniteSampleColumn.

biomeUtils 0.011

• Handle missing tree in clusterASVs.
• Added renameSampleVariables.
• Fix pipe section in vignette.

biomeUtils 0.010

• Fixes to getSampleTibble.
• Fixes to getPrevalence.
• Fixes to calculateTaxaFoldDifference.

biomeUtils 0.0.09

• Added mutatePhyloseq functions added.
• Added checkPolyphyletic functions added.
• Minor fixes in documentations.

biomeUtils 0.0.08

• Added meltDistanceToTable fix.

biomeUtils 0.0.07

• Added getPrevalence fix.
• Vignette addition pipes example.

biomeUtils 0.0.06

• Added getPhyloseqSlots functions.
• Added filterPhyloseq functions.
• Improved removeZeros.
• Added clusterASVs ASVs to OTUs.
• Added calculateQC Calculate QC metrics for taxa and samples.

biomeUtils 0.0.05

• Added buildSeqTree to build trees from sequences.
• Added calculateTaxaFoldDifference to build trees from sequences.
• Added cleanTaxonomy to build trees from sequences.
• Added getPrevalence
• Added calculatePD

biomeUtils 0.0.04

• Added getTaxaSummary.
• Added removeZeros.
• Added saveSequence.
• Added summarizeTaxonomicAssignments.
• Added trendAbundanceAssignment.
• Added SprockettTHData example data.

biomeUtils 0.0.03

• Added comparePhyloseq to compare phyloseq objects.
• Added getTibbles create tibbles from phyloseq objects.
• Added uniteGenusSpeciesNames.

biomeUtils 0.0.02

• Added a NEWS.md file to track changes to the package.

biomeUtils 0.0.01

• Added FuentesIliGutData example data.
• First build of the package.

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.