R Observatory: Metrics for TaxaNorm version 2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TaxaNorm

2.4Package record

Feature-Wise Normalization for Microbiome Sequencing Data

0packages depend

1.7Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Dillon LloydCRAN page ↗GitHub ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

4ERROR9OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

ERRORwhether package can be installedr-oldrel-windows-x86_64, r-release-windows-x86_64

r-oldrel-windows-x86_64

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/TaxaNorm.Rcheck/00install.out' for details.

r-release-windows-x86_64

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/TaxaNorm.Rcheck/00install.out' for details.

CRAN check page ↗

Slowest check: 5.8 min · r-devel-windows-x86_64

Status changes

ERROR9 OK, 4 ERRORNow
ERROR8 OK, 6 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4

READMEYes · 77 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 2.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 10 (1 internal)includes a package overview page
Examples that run: 50%4 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 71%
Help pages citing references: 0%

Vignettes (1)

TaxNorm Introduction

How these are measured

Downloads

1.7K

CRAN downloads in the past year

Rank #24,219 · ~5/day · ~144/mo

Releases R versions

Daily download trend is not available in this view yet.

21830 days

50690 days

1.7K1 year

Compare downloads with other packages →

Also on70 r2u

How downloads are counted

Repository

wangziyue57/taxanorm ↗Account: wangziyue57

0Stars

0Forks

3Open issues

0Open PRs

0Releases

Last activity 2025-11-19 · The default branch showed an older version (2.3) than CRAN on 2026-10-18

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: not measured

How these are measured

PracticesBeta

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

Checks run against github.com/wangziyue57/taxanorm on 2026-10-18.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing TaxaNorm adds 27 packages (12 with compiled code, 19 MB of source tarballs). Heaviest: ggplot2 6.0 MB, pscl 2.9 MB, isoband 1.5 MB. 4 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Dillon Lloyd

Alison Motsinger-Reif

Author, Contributor

Ziyue Wang

Author

Shanshan Zhao

Author, Contributor

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.4Latest
record
2023-12-12 · current release
R
R 4.3.0 released · 2023-04-21

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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →