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ensembleTax (version 1.1.1)

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

1.1.1

License

MIT + file LICENSE

Maintainer

Dylan Catlett

Last Published

May 21st, 2021

Functions in ensembleTax (1.1.1)

assign.ensembleTax

Computes ensemble taxonomic assignments for each ASV in an amplicon data set
idtax.pr2.sample

Example output of DECIPHER idtaxa function with pr2 taxonomy
bayestax2df

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

Example output of DECIPHER idtaxa function with silva taxonomy
gg_13_8_train_set_97

All unique taxonomic assignments from the GreenGenes v13.8 clusted at 97%
synonyms_v2

Taxonomic synonyms searched by the taxmapper algorithm
idtax2df

Converts outputs of DECIPHER's idtaxa algorithm into a dataframe compatible with the algorithms used in ensembleTax.
pr2v4.12.0

All unique taxonomic assignments from the pr2 reference database v4.12.0
rdp_train_set_16

All unique taxonomic assignments from the RDP Train Set 16
rubric.sample

Example rubric with ASV-identifying data
taxmapper

Maps an input taxonomy table onto a different taxonomic nomenclature.
bayes.sample

Example output of dada2 assignTaxonomy function
sort_my_taxtab

Sorts taxonomy table by ASV-identifying columns.
silva.nr.v138

All unique taxonomic assignments from the Silva SSU nr database v138