Other packages > Find by keyword >

demulticoder  

Simultaneous Analysis of Multiplexed Metabarcodes
View on CRAN: Click here


Download and install demulticoder package within the R console
Install from CRAN:
install.packages("demulticoder")

Install from Github:
library("remotes")
install_github("cran/demulticoder")

Install by package version:
library("remotes")
install_version("demulticoder", "0.1.2")



Attach the package and use:
library("demulticoder")
Maintained by
Martha A. Sudermann
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-05-05
Latest Update: 2025-05-05
Description:
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>.
How to cite:
Martha A. Sudermann (2025). demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes. R package version 0.1.2, https://cran.r-project.org/web/packages/demulticoder. Accessed 07 Mar. 2026.
Previous versions and publish date:
No previous versions
Other packages that cited demulticoder R package
View demulticoder citation profile
Other R packages that demulticoder depends, imports, suggests or enhances
Complete documentation for demulticoder
Functions, R codes and Examples using the demulticoder R package
Full demulticoder package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

ReviewR  
A Light-Weight, Portable Tool for Reviewing Individual Patient Records
A portable Shiny tool to explore patient-level electronic health record data and perform chart revi ...
Download / Learn more Package Citations See dependency  
testDriveR  
Teaching Data for Statistics and Data Science
Provides data sets for teaching statistics and data science courses. It includes a sample of data f ...
Download / Learn more Package Citations See dependency  
portalr  
Create Useful Summaries of the Portal Data
Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Projec ...
Download / Learn more Package Citations See dependency  
SAMtool  
Stock Assessment Methods Toolkit
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
lmSubsets  
Exact Variable-Subset Selection in Linear Regression
Exact and approximation algorithms for variable-subset selection in ordinary linear regression mode ...
Download / Learn more Package Citations See dependency  

26,264

R Packages

223,360

Dependencies

70,376

Author Associations

26,265

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA