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ensembleTax (version 1.0.2)

Ensemble Taxonomic Assignments of Amplicon Sequencing Data

Description

Creates ensemble taxonomic assignments of amplicon sequencing data in R using outputs of multiple taxonomic assignment algorithms and/or reference databases. Includes flexible algorithms for mapping taxonomic nomenclatures onto one another and for computing ensemble taxonomic assignments.

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Version

Install

install.packages('ensembleTax')

Monthly Downloads

210

Version

1.0.2

License

MIT + file LICENSE

Maintainer

Dylan Catlett

Last Published

January 11th, 2021

Functions in ensembleTax (1.0.2)

Example rubric with ASV-identifying data

Computes ensemble taxonomic assignments for each ASV in an amplicon data set

Converts outputs of DECIPHER's idtaxa algorithm into a dataframe compatible with the algorithms used in ensembleTax.

gg_13_8_train_set_97

All unique taxonomic assignments from the GreenGenes v13.8 clusted at 97%

Example output of dada2 assignTaxonomy function

idtax.pr2.sample

Example output of DECIPHER idtaxa function with pr2 taxonomy

idtax.silva.sample

Example output of DECIPHER idtaxa function with silva taxonomy

All unique taxonomic assignments from the pr2 reference database v4.12.0

All unique taxonomic assignments from the Silva SSU nr database v138

synonyms_20200816

Taxonomic synonyms searched by the taxmapper algorithm

rdp_train_set_16

All unique taxonomic assignments from the RDP Train Set 16

Sorts taxonomy table by ASV-identifying columns.

Converts the output of DADA2's assignTaxonomy, which implements a naive bayesian classifier, into a dataframe compatible with the algorithms used in ensembleTax

Maps an input taxonomy table onto a different taxonomic nomenclature.