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AmpliconDuo
View on CRAN: Click
here
Download and install AmpliconDuo package within the R console
Install from CRAN:
install.packages("AmpliconDuo")
Install from Github:
library("remotes")
install_github("cran/AmpliconDuo")
Install by package version:
library("remotes")
install_version("AmpliconDuo", "1.1.1")
Attach the package and use:
library("AmpliconDuo")
Maintained by
Anja Lange
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-03-20
Latest Update: 2020-05-25
Description:
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.
How to cite:
Anja Lange (2014). AmpliconDuo: Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts. R package version 1.1.1, https://cran.r-project.org/web/packages/AmpliconDuo
Other packages that cited AmpliconDuo R package
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Other R packages that AmpliconDuo depends,
imports, suggests or enhances
Functions, R codes and Examples using
the AmpliconDuo R package
Some associated functions: AmpliconDuo-package . accepted.amplicons . ampliconduo . ampliconfreqs.long . ampliconfreqs . amplicons . discordance.delta . filter.ampliconduo . filter.ampliconduo.set . plotAmpliconduo . plotAmpliconduo.set . plotORdensity . site.f .
Some associated R codes: accepted.amplicons.R . ampliconduo.R . discordance.delta.R . filter.ampliconduo.R . filter.ampliconduo.set.R . plotAmpliconduo.R . plotAmpliconduo.set.R . plotORdensity.R . Full AmpliconDuo package functions and examples
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