Package: ensembleTax 1.1.1

Dylan Catlett

ensembleTax: Ensemble Taxonomic Assignments of Amplicon Sequencing Data

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.

Authors:Dylan Catlett [aut, cre], Kevin Son [ctb], Connie Liang [ctb]

ensembleTax_1.1.1.tar.gz
ensembleTax_1.1.1.tar.gz(r-4.5-noble)ensembleTax_1.1.1.tar.gz(r-4.4-noble)
ensembleTax_1.1.1.tgz(r-4.4-emscripten)ensembleTax_1.1.1.tgz(r-4.3-emscripten)
ensembleTax.pdf |ensembleTax.html✨
ensembleTax/json (API)

# Install 'ensembleTax' in R:
install.packages('ensembleTax', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • bayes.sample - Example output of dada2 assignTaxonomy function
  • gg_13_8_train_set_97 - All unique taxonomic assignments from the GreenGenes v13.8 clusted at 97%
  • idtax.pr2.sample - Example output of DECIPHER idtaxa function with pr2 taxonomy
  • idtax.silva.sample - Example output of DECIPHER idtaxa function with silva taxonomy
  • 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
  • silva.nr.v138 - All unique taxonomic assignments from the Silva SSU nr database v138
  • synonyms_v2 - Taxonomic synonyms searched by the taxmapper algorithm

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

5 exports 0.23 score 72 dependencies 1 mentions 5 scripts 251 downloads

Last updated 3 years agofrom:62d14848b5. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 23 2024
R-4.5-linuxNOTEAug 23 2024

Exports:assign.ensembleTaxbayestax2dfidtax2dfsort_my_taxtabtaxmapper

Dependencies:askpassBiocGenericsBiostringsclicliprcolorspacecrayoncredentialscurlDBIDECIPHERdescdplyrfansifarverfsgenericsGenomeInfoDbGenomeInfoDbDatagertggplot2ghgitcredsgluegtablehttrhttr2iniIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpurrrR6rappdirsRColorBrewerRcppreshape2rlangrprojrootrstudioapiS4VectorsscalesstringistringrsystibbletidyselectUCSC.utilsusethisutf8vctrsviridisLitewhiskerwithrXVectoryamlzipzlibbioc

assign.ensembleTax tutorial

D Catlett

Rendered fromassign.ensembleTax_tutorial.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2021-05-21
Started: 2021-05-21

ensembleTax package vignette

D Catlett

Rendered fromensembleTax.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2021-05-21
Started: 2021-01-11

taxmapper tutorial

D Catlett

Rendered fromtaxmapper_tutorial.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2021-05-21
Started: 2021-05-21