Last data update: 2014.03.03

AmpliconDuo

Package: AmpliconDuo
Type: Package
Title: Statistical Analysis of Amplicon Data of the Same Sample to
Identify Artefacts
Authors@R: c(person(given = "Anja", family = "Lange", role =
c("aut", "cre"), email = "anja.lange@uni-due.de"),
person(given = "Daniel", family = "Hoffmann", role = "aut", email
= "daniel.hoffmann@uni-due.de"))
Version: 1.1
Date: 2016-01-14
Author: Anja Lange [aut, cre], Daniel Hoffmann [aut]
Maintainer: Anja Lange <anja.lange@uni-due.de>
Depends: R (>= 2.10), stats, ggplot2, xtable
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.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2016-01-19 09:46:32 UTC; anja
Repository: CRAN
Date/Publication: 2016-01-19 13:09:23

13 images, 9 functions, 4 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'AmpliconDuo' ...
** package 'AmpliconDuo' successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'AmpliconDuo'
    finding HTML links ... done
    AmpliconDuo-package                     html  
    accepted.amplicons                      html  
    ampliconduo                             html  
    ampliconfreqs                           html  
    ampliconfreqs.long                      html  
    amplicons                               html  
    discordance.delta                       html  
    filter.ampliconduo                      html  
    filter.ampliconduo.set                  html  
    plotAmpliconduo                         html  
    plotAmpliconduo.set                     html  
    plotORdensity                           html  
    site.f                                  html  
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (AmpliconDuo)
Making 'packages.html' ... done