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AmpliconDuo

1.1.1

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

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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.

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Health

CRAN checks
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Code health
None
Tests · ratio 0.00
not tracked
Coverage
100%
Documentation · exports
None
Vignettes
No
README
3
Dependencies · direct
Check history
  • NOTE2026-03-10
    0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

3.3K
CRAN downloads in the past year
Rank #13,610 · ~9/day · ~273/mo
32530 days
79390 days
3.3K1 year
Also on108 r2u61 autocran1.3K conda_forge191 bioconda
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Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies
2 external dependencies (excludes base and recommended)
Depends (4)
R >= 2.10stats baseggplot2xtable
Imports (0)
none
LinkingTo (0)
none
Suggests (0)
none
Enhances (0)
none
Reverse dependencies
0direct
–indirect (not tracked)

Nothing depends on this yet.

Code

1,500Lines of code
8Exported functions

Code & tests

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Line coverage

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Expression

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Tests / Examples

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Functions

8 8 exported

Complexity

7.3 avg / 14 max

Call network

8 nodes / 0 edges

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)
Maintainer (1)
Anja Lange
Author, Maintainer
Authors (1)
Daniel Hoffmann
Author
Release 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
  • R
    R 4.0.0 released · 2020-04-24
  • 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
  • R
    R 3.1.0 released · 2014-04-10
  • 1.0
    2014-03-20

Package metadata

First published
2014-03-20
Total releases
3 / 12 yrs
License
GPL (>= 3) OSI
Download size
not tracked yet
Installed size
not tracked yet
With dependencies
not tracked yet