Package: AmpliconDuo 1.1.1
AmpliconDuo: Statistical Analysis of Amplicon Data of the Same Sample to Identify Artefacts
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.
Authors:
AmpliconDuo_1.1.1.tar.gz
AmpliconDuo_1.1.1.zip(r-4.5)AmpliconDuo_1.1.1.zip(r-4.4)AmpliconDuo_1.1.1.zip(r-4.3)
AmpliconDuo_1.1.1.tgz(r-4.4-any)AmpliconDuo_1.1.1.tgz(r-4.3-any)
AmpliconDuo_1.1.1.tar.gz(r-4.5-noble)AmpliconDuo_1.1.1.tar.gz(r-4.4-noble)
AmpliconDuo_1.1.1.tgz(r-4.4-emscripten)AmpliconDuo_1.1.1.tgz(r-4.3-emscripten)
AmpliconDuo.pdf |AmpliconDuo.html✨
AmpliconDuo/json (API)
| # Install 'AmpliconDuo' in R: |
| install.packages('AmpliconDuo', repos = c('https://anla8000.r-universe.dev', 'https://cloud.r-project.org')) |
- ampliconfreqs - SSU Amplicon Frequencies Of Different Sampling Sites
- ampliconfreqs - SSU Amplicon Frequencies Of Different Sampling Sites
- amplicons - Example List of Ampliconduo Data Frames
- site.f - Sampling Site Short Names
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:62025005eb. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-win | NOTE | Aug 28 2024 |
| R-4.5-linux | NOTE | Aug 28 2024 |
| R-4.4-win | NOTE | Aug 28 2024 |
| R-4.4-mac | NOTE | Aug 28 2024 |
| R-4.3-win | OK | Aug 28 2024 |
| R-4.3-mac | OK | Aug 28 2024 |
Exports:accepted.ampliconsampliconduodiscordance.deltafilter.ampliconduofilter.ampliconduo.setplotAmpliconduoplotAmpliconduo.setplotORdensity
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Statistical Analysis Of Amplicon Data Of The Same Sample To Identify Spurious Amplicons | AmpliconDuo-package AmpliconDuo |
| List Of Amplicon Indices That Passed Filter Criteria | accepted.amplicons |
| Apply Fisher's Exact Tests To Two Amplicon Frequency Sets Of The Same Sample | ampliconduo |
| SSU Amplicon Frequencies Of Different Sampling Sites (Short Version) | ampliconfreqs |
| SSU Amplicon Frequencies Of Different Sampling Sites | ampliconfreqs.long |
| Example List of Ampliconduo Data Frames | amplicons |
| Measure Of Discordance Between Two Amplicon Data Sets | discordance.delta |
| AmpliconDuo Amplicon Filter | filter.ampliconduo |
| AmpliconDuo List Amplicon Filter | filter.ampliconduo.set |
| Frequeny-Frequency Plot Focusing On Significant Deviations In Amplicon Occurences | plotAmpliconduo |
| Frequeny-Frequency Plot Arrangement Focusing On Significant Deviations In Amplicon Occurences | plotAmpliconduo.set |
| Probability Density Plot Of Odds Ratios | plotORdensity |
| Sampling Site Short Names | site.f |
