Package: TaxaNorm 2.3

Dillon Lloyd

TaxaNorm: Feature-Wise Normalization for Microbiome Sequencing Data

A novel feature-wise normalization method based on a zero-inflated negative binomial model. This method assumes that the effects of sequencing depth vary for each taxon on their mean and also incorporates a rational link of zero probability and taxon dispersion as a function of sequencing depth. Ziyue Wang, Dillon Lloyd, Shanshan Zhao, Alison Motsinger-Reif (2023) <doi:10.1101/2023.10.31.563648>.

Authors:Ziyue Wang [aut], Dillon Lloyd [aut, cre, cph], Shanshan Zhao [aut, ctb], Alison Motsinger-Reif [aut, ctb]

TaxaNorm_2.3.tar.gz
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TaxaNorm.pdf |TaxaNorm.html✨
TaxaNorm/json (API)
NEWS

# Install 'TaxaNorm' in R:
install.packages('TaxaNorm', repos = c('https://wangziyue57.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/wangziyue57/taxanorm/issues

Datasets:

On CRAN:

sequencingmicrobiomemetagenomicsnormalizationvisualization

4.00 score 2 scripts 127 downloads 31 exports 92 dependencies

Last updated 12 months agofrom:2dcf392e11. Checks:OK: 6 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-winOKNov 07 2024
R-4.5-linuxWARNINGNov 07 2024
R-4.4-winOKNov 07 2024
R-4.4-macOKNov 07 2024
R-4.3-winOKNov 07 2024
R-4.3-macOKNov 07 2024

Exports:coefficientscoefficients<-convergeconverge<-ecdfecdf<-final_dffinal_df<-input_datainput_data<-llkllk<-model_parsmodel_pars<-mumu<-normdatanormdata<-pipi<-rawdatarawdata<-TaxaNorm_Model_ParametersTaxaNorm_Model_QCTaxaNorm_NMDSTaxaNorm_NormalizationTaxaNorm_QC_InputTaxaNorm_ResultsTaxaNorm_Run_Diagnosethetatheta<-

Dependencies:ade4apeaskpassbayesmBiobaseBiocGenericsbiomformatBiostringscliclustercodetoolscolorspacecompositionscpp11crayoncurldata.tableDEoptimRdigestdplyrfansifarverforeachfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggplot2globalsgluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelistenvmagrittrMASSMatrixmatrixStatsmgcvmicrobiomemimemulttestmunsellnlmeopensslparallellypermutephyloseqpillarpixmappkgconfigplyrpsclpurrrR6RColorBrewerRcppRcppArmadilloreshape2rhdf5rhdf5filtersRhdf5librlangrobustbaseRtsneS4VectorsscalesspstringistringrsurvivalsystensorAtibbletidyrtidyselectUCSC.utilsutf8vctrsveganviridisLitewithrXVectorzlibbioc

TaxNorm Introduction

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2023-10-24
Started: 2023-10-09

Readme and manuals

Help Manual

Help pageTopics
TaxaNorm_Model_Parameterscoefficients,TaxaNorm_Model_Parameters-method coefficients<-,TaxaNorm_Model_Parameters-method mu,TaxaNorm_Model_Parameters-method mu<-,TaxaNorm_Model_Parameters-method pi,TaxaNorm_Model_Parameters-method pi<-,TaxaNorm_Model_Parameters-method TaxaNorm_Model_Parameters TaxaNorm_Model_Parameters-class TaxaNorm_Model_Parameters-coefficients TaxaNorm_Model_Parameters-mu TaxaNorm_Model_Parameters-pi TaxaNorm_Model_Parameters-theta theta,TaxaNorm_Model_Parameters-method theta<-,TaxaNorm_Model_Parameters-method
Function to QC TaxNorm algorithmTaxaNorm_Model_QC
Function for TaxNorm NMDSTaxaNorm_NMDS
Function to run TaxaNorm algorithmTaxaNorm_Normalization
Function for TaxNorm input dataTaxaNorm_QC_Input
TaxaNorm Resultsconverge,TaxaNorm_Results-method converge<-,TaxaNorm_Results-method ecdf,TaxaNorm_Results-method ecdf<-,TaxaNorm_Results-method final_df,TaxaNorm_Results-method final_df<-,TaxaNorm_Results-method input_data,TaxaNorm_Results-method input_data<-,TaxaNorm_Results-method llk,TaxaNorm_Results-method llk<-,TaxaNorm_Results-method model_pars,TaxaNorm_Results-method model_pars<-,TaxaNorm_Results-method normdata,TaxaNorm_Results-method normdata<-,TaxaNorm_Results-method rawdata,TaxaNorm_Results-method rawdata<-,TaxaNorm_Results-method TaxaNorm_Results TaxaNorm_Results-class TaxaNorm_Results-converge TaxaNorm_Results-ecdf TaxaNorm_Results-final_df TaxaNorm_Results-input_data TaxaNorm_Results-llk TaxaNorm_Results-model_pars TaxaNorm_Results-normdata TaxaNorm_Results-rawdata
Function to run TaxNorm algorithmTaxaNorm_Run_Diagnose
TaxaNorm data objectsTaxaNorm-datasets TaxaNorm_Example_Input TaxaNorm_Example_Output
TaxaNorm package genericscoefficients coefficients<- converge converge<- ecdf ecdf<- final_df final_df<- input_data input_data<- llk llk<- model_pars model_pars<- mu mu<- normdata normdata<- pi pi<- rawdata rawdata<- TaxaNormGenerics theta theta<-