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otuSummary (version 0.1.1)

Summarizing OTU Table Regarding the Composition, Abundance and Beta Diversity of Abundant and Rare Biospheres

Description

Summarizes the taxonomic composition, diversity contribution of the rare and abundant community by using OTU (operational taxonomic unit) table which was generated by analyzing pipeline of 'QIIME' or 'mothur'. The rare biosphere in this package is subset by the relative abundance threshold (for details about rare biosphere please see Lynch and Neufeld (2015) ).

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Install

install.packages('otuSummary')

Monthly Downloads

305

Version

0.1.1

License

GPL (>= 3)

Issues

0

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Forks

1

Maintainer

Sizhong Yang

Last Published

March 31st, 2020

Functions in otuSummary (0.1.1)

rareBiosphere

Summarize different subgroups in the rare biosphere
subOTU

Subset a OTU table
typeConvert

Transpose the data frame if there is data type conversion.
otumothur

OTU table generated from 8 lakes over 4 years
contrib

Contribution of rare/abundant biosphere to the total Bray-Curtis dissimilarity
pbray

Partition the Bray-Curtis distance dissimilarity
otu4type

An example OTU table with samples and taxonomy in rows and otus in columns
ordination

Quickly check the constrained or unconstrained ordination plot
alphaDiversity

Calculate the alpha diversity indices
matrixConvert

Convert lower triangular distance matrix into data frame
otuReport

Summarize the community structure and abundance with OTU table
otuCollap

collapse a OTU table at given level.
otuqiime

OTU table generated from 8 lakes over 4 years