Introduction | What is the ZINB method? | Outline | Installation | Required Packages | Installation from Bioconductor | Installation from Github | Loading Package into R Environment | Example Usage | Load Input Data | Pre-process Input Data | QC Input Data | Run Normalization | QC TaxNorm Model | TaxNorm NMDS
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:
TaxaNorm_2.3.tar.gz
TaxaNorm_2.3.zip(r-4.7)TaxaNorm_2.3.zip(r-4.6)TaxaNorm_2.3.zip(r-4.5)
TaxaNorm_2.3.tgz(r-4.6-any)TaxaNorm_2.3.tgz(r-4.5-any)
TaxaNorm_2.3.tar.gz(r-4.7-any)TaxaNorm_2.3.tar.gz(r-4.6-any)
TaxaNorm_2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TaxaNorm/json (API)
| # Install 'TaxaNorm' in R: |
| install.packages('TaxaNorm', repos = c('https://wangziyue57.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wangziyue57/taxanorm/issues
Datasets:
- TaxaNorm_Example_Input - TaxaNorm data objects
- TaxaNorm_Example_Output - TaxaNorm data objects
sequencingmicrobiomemetagenomicsnormalizationvisualization
Last updated from:4cf01e5c2b. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 240 | ||
| source / vignettes | OK | 210 | ||
| linux-release-x86_64 | OK | 201 | ||
| macos-release-arm64 | OK | 239 | ||
| macos-oldrel-arm64 | OK | 225 | ||
| windows-devel | OK | 178 | ||
| windows-release | OK | 194 | ||
| windows-oldrel | OK | 192 | ||
| wasm-release | OK | 127 |
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:ade4apebayesmBiobaseBiocGenericsbiomformatBiostringscliclustercodetoolscompositionscpp11crayondata.tableDEoptimRdigestdplyrfarverforeachfuturefuture.applygenericsggplot2globalsgluegtableigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelistenvmagrittrMASSMatrixmatrixStatsmgcvmicrobiomemulttestnlmeparallellypermutephyloseqpillarpixmappkgconfigplyrpsclpurrrR6RColorBrewerRcppRcppArmadilloreshape2rlangrobustbaseRtsneS4VectorsS7scalesSeqinfospstringistringrsurvivaltensorAtibbletidyrtidyselectutf8vctrsveganviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| TaxaNorm_Model_Parameters | coefficients,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 algorithm | TaxaNorm_Model_QC |
| Function for TaxNorm NMDS | TaxaNorm_NMDS |
| Function to run TaxaNorm algorithm | TaxaNorm_Normalization |
| Function for TaxNorm input data | TaxaNorm_QC_Input |
| TaxaNorm Results | converge,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 algorithm | TaxaNorm_Run_Diagnose |
| TaxaNorm data objects | TaxaNorm-datasets TaxaNorm_Example_Input TaxaNorm_Example_Output |
| TaxaNorm package generics | coefficients 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<- |