CRAN requires the check problems on this package to be fixed before 2026-08-31 or it will be archived.

AmpliconDuo

1.1.1

Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts

0packages depend

3.2Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Anja LangeFirst published 2014-03-203 releasesCRAN page ↗

Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

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-ampliconduo

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-AmpliconDuo

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# 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-AmpliconDuo

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 2.5 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 63%
References docs: 62%

Downloads

3.2K

CRAN downloads in the past year

Rank #12,542 · ~9/day · ~270/mo

Releases R versions

Daily download trend is not available in this view yet.

28230 days

80990 days

3.2K1 year

Compare downloads with other packages →

Also on116 r2u6 autocran1.3K conda_forge191 bioconda

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (4)

R >= 2.10statsggplot2 xtable

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Anja Lange

Author, Maintainer

Authors (2)

Anja Lange

Author, Maintainer

Daniel Hoffmann

Author

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.1Latest
2020-05-26 · current release · diff ↗
unarchivedReturned to CRAN
2020-05-26
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-01-14
check errors were not corrected in time Detritus with variable names
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.1
2016-01-19 · diff ↗
R
R 3.2.0 released · 2015-04-16

Show 3 earlier events

R
R 3.1.0 released · 2014-04-10
1.0
2014-03-20
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2014-03-20
Total releases: 3 / 12 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 447 KB / 4 files
Download size: 483 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →