Tidyamplicons is a R package for the exploration of microbial community data. Such community data consists of read counts generated by amplicon sequencing (e.g. a region of the 16S rRNA gene) or metagenome (shotgun) sequencing. Each read count represents a number of sequencing reads identified for some taxon (an OTU, ASV, species, or higher-level taxon) in a sample.
Tidyamplicons builds on the tidyverse created by Hadley Wickham: the data are stored in tidy tables where each row is an observation and each column a variable. In addition, the package supplies a set of "verbs": functions that take a tidyamplicons object as first argument and also return a tidyamplicons object.
Tidyamplicons is an R package. You can find instructions to download and install R here.
Tidyamplicons relies on the tidyverse R package (or, more accurately, set of R packages). You can install the tidyverse by running the following R code:
install.packages("tidyverse")Finally, RStudio is a nice IDE to work with R code (as well as code in other scripting languages). It has a lot more features than what the default R IDE allows: beyond creating and saving scripts, it also shows your figures, allows you to navigate files, allows you to inspect tables etc. You can download RStudio here.
Run the following R code to install the latest version of tidyamplicons:
install.packages("devtools")
devtools::install_github("SWittouck/tidyamplicons")A documentation page (help page) is available for all functions. You can view it by running e.g. ?filter_samples. For most functions it is still very basic; this will be improved in the future. Some useful tutorials can be found on the wiki.