R library to generate 'Cumulative Percent Decay' curves for microbial taxonomic profiles

cuperdec

R package to generate 'Cumulative Percent Decay' curves, with optional filtering functions, for microbial taxonomic profiles.

These curves aim to represent the level of 'endogenous' content of microbiome samples, such as ancient dental calculus, to help to identify samples with lowlevels of preservation that should be discarded for downstream analysis.

Installation

cuperdec is on CRAN. You can install the package with the usual command

rinstall.packages("cuperdec")

To install the development version for testing, you can runthe following

```r

install.packages("devtools")

devtools::install_github("jfy133/cuperdec")```

Documentation

Please see vignettes/cuperdec-intro.Rmd.

Citation

If you use cuperdec, please use the following citation:

Fellows Yates, J. A. et al. (2021) ‘The evolution and changing ecology of the African hominid oral microbiome’, Proceedings of the National Academy of Sciences of the United States of America, 118(20), p. e2021655118. doi: 10.1073/pnas.2021655118.

Acknowledgments

Irina Velsko (@ivelsko), Zandra Fagerness (@ZandraFagernas), and Lena Semerau for testing and bug reports.

To restore the repository download the bundle

wget https://archive.org/download/github.com-jfy133-cuperdec_-_2021-05-19_08-50-20/jfy133-cuperdec_-_2021-05-19_08-50-20.bundle

and run:

 git clone jfy133-cuperdec_-_2021-05-19_08-50-20.bundle 

Source: https://github.com/jfy133/cuperdec
Uploader: jfy133
Upload date: 2021-05-19

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