R Observatory: Metrics for TaxaNorm version 2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TaxaNorm

2.4

Feature-Wise Normalization for Microbiome Sequencing Data

0packages depend

1.5Kdownloads / year

–test coverage

10/13checks pass

Overview

About

Maintained by Dillon LloydFirst published 2023-12-121 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("TaxaNorm", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("wangziyue57/TaxaNorm")

Development version from wangziyue57/TaxaNorm. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-taxanorm

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

3ERROR10OK

Failing flavors

ERROR r-oldrel-macos-arm64
ERROR r-oldrel-macos-x86_64
ERROR r-release-windows-x86_64

Slowest check: 5.9 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

15

Dependencies · direct

Check history

ERROR2026-03-10
8 OK · 0 NOTE · 0 WARNING · 6 ERROR · 0 FAILURE

Documentation

READMEYes · 77 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: 100%
Return-value docs: 71%
References docs: 0%

Downloads

1.5K

CRAN downloads in the past year

Rank #22,734 · ~4/day · ~127/mo

Releases R versions

Daily download trend is not available in this view yet.

9630 days

46790 days

1.5K1 year

Compare downloads with other packages →

Also on98 r2u

Repository

GitHub ↗ wangziyue57/taxanorm

0Stars

0Forks

3Open issues

0Open PRs

0Releases

Last activity 2025-11-19

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/wangziyue57/taxanorm on 2026-08-16.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.0.0microbiome

Imports (14)

phyloseqstatsS4Vectors BiocGenerics veganmethodsMASSfuture future.apply matrixStats pscl parallelly ggplot2utils

LinkingTo (0)

none

Suggests (2)

rmarkdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Dillon Lloyd

Author, Maintainer, Copyright holder

Authors (4)

Dillon Lloyd

Author, Maintainer, Copyright holder

Alison Motsinger-Reif

Author, Contributor

Ziyue Wang

Author

Shanshan Zhao

Author, Contributor

Contributors (2)

Alison Motsinger-Reif

Author, Contributor

Shanshan Zhao

Author, Contributor

Copyright holders (1)

Dillon Lloyd

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.4Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2023-12-12
Total releases: 1 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 515 KB / 2 files
Download size: 581 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("TaxaNorm")

Format

Lloyd, D., Motsinger-Reif, A., Wang, Z., & Zhao, S. (2023). TaxaNorm: Feature-Wise Normalization for Microbiome Sequencing Data (Version 2.4) [Computer software]. https://doi.org/10.32614/CRAN.package.TaxaNorm

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for TaxaNorm version 2.4 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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