Microbiome datasets are compositional: and this is not optional
Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers,
metagenomes or metatranscriptomes are commonplace and being used to study human …
metagenomes or metatranscriptomes are commonplace and being used to study human …
[HTML][HTML] Network analysis methods for studying microbial communities: A mini review
MS Matchado, M Lauber, S Reitmeier… - Computational and …, 2021 - Elsevier
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities
in complex and contiguous environments. They engage in numerous inter-and intra …
in complex and contiguous environments. They engage in numerous inter-and intra …
Understanding sequencing data as compositions: an outlook and review
Motivation Although seldom acknowledged explicitly, count data generated by sequencing
platforms exist as compositions for which the abundance of each component (eg gene or …
platforms exist as compositions for which the abundance of each component (eg gene or …
A field guide for the compositional analysis of any-omics data
Background Next-generation sequencing (NGS) has made it possible to determine the
sequence and relative abundance of all nucleotides in a biological or environmental …
sequence and relative abundance of all nucleotides in a biological or environmental …
[HTML][HTML] propr: an R-package for identifying proportionally abundant features using compositional data analysis
In the life sciences, many assays measure only the relative abundances of components in
each sample. Such data, called compositional data, require special treatment to avoid …
each sample. Such data, called compositional data, require special treatment to avoid …
Compositional data analysis
M Greenacre - Annual Review of Statistics and its Application, 2021 - annualreviews.org
Compositional data are nonnegative data carrying relative, rather than absolute, information—
these are often data with a constant-sum constraint on the sample values, for example …
these are often data with a constant-sum constraint on the sample values, for example …
The gut microbiota of healthy aged Chinese is similar to that of the healthy young
The microbiota of the aged is variously described as being more or less diverse than that of
younger cohorts, but the comparison groups used and the definitions of the aged population …
younger cohorts, but the comparison groups used and the definitions of the aged population …
Compositional data: the sample space and its structure
The log-ratio approach to compositional data (CoDa) analysis has now entered a mature
phase. The principles and statistical tools introduced by J. Aitchison in the eighties have …
phase. The principles and statistical tools introduced by J. Aitchison in the eighties have …
[HTML][HTML] Population-level configurations of gut mycobiome across 6 ethnicities in urban and rural China
Abstract Background & Aims Beyond bacteria, the human gastrointestinal tract is host to a
vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact …
vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact …
Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods
The tremendous boost in next generation sequencing and in the “omics” technologies
makes it possible to characterize the human gut microbiome—the collective genomes of the …
makes it possible to characterize the human gut microbiome—the collective genomes of the …