demulticoder

0.1.2

Simultaneous Analysis of Multiplexed Metabarcodes

0packages depend

5.8Kdownloads / year

2.7%test coverage

13/13checks pass

Overview

About

Maintained by Martha A. SudermannFirst published 2025-05-051 releasesCRAN page ↗GitHub ↗

A comprehensive set of wrapper functions for the analysis of multiplex metabarcode data. It includes robust wrappers for 'Cutadapt' and 'DADA2' to trim primers, filter reads, perform amplicon sequence variant (ASV) inference, and assign taxonomy. The package can handle single metabarcode datasets, datasets with two pooled metabarcodes, or multiple datasets simultaneously. The final output is a matrix per metabarcode, containing both ASV abundance data and associated taxonomic assignments. An optional function converts these matrices into 'phyloseq' and 'taxmap' objects. For more information on 'DADA2', including information on how DADA2 infers samples sequences, see Callahan et al. (2016) doi:10.1038/nmeth.3869. For more details on the demulticoder R package see Sudermann et al. (2025) doi:10.1094/PHYTO-02-25-0043-FI.

Install

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

install.packages("demulticoder", 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("grunwaldlab/demulticoder")

Development version from grunwaldlab/demulticoder. 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-demulticoder

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-demulticoder

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

5.8K

CRAN downloads in the past year

Rank #8,018 · ~16/day · ~482/mo

demulticoder Releases R versions

Daily download trend is not available in this view yet.

30230 days

1.3K90 days

5.8K1 year

Compare downloads with other packages →

Also on120 r2u25 autocran

Repository

GitHub ↗ grunwaldlab/demulticoder

1Stars

0Forks

2Open issues

0Open PRs

0Releases

615Commits

51Contributors

615 commits · Last activity 2025-06-13

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/grunwaldlab/demulticoder on 2026-07-19.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.2

Imports (9)

furrr purrr readr stringr tidyr dplyr ggplot2 tibbleutils

LinkingTo (0)

none

Suggests (9)

BiocManager Biostrings dada2 metacoder ShortRead phyloseq rmarkdown RcppParallel testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Martha A. Sudermann

Author, Maintainer, Copyright holder

Authors (6)

Martha A. Sudermann

Author, Maintainer, Copyright holder

Samantha Dawson

Author

Zachary S. L Foster

Author

Niklaus Grünwald

Author, Copyright holder

Jeff H. Chang

Author

Hung Phan

Author

Martha A. Sudermann

Author, Maintainer, Copyright holder

Niklaus Grünwald

Author, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.2Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-05
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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