My R package QsRutils is now on CRAN as version 0.2.1. You may install it in R with install.packages(“QsRutils”) or by using the menu in RStudio to install from CRAN.
Version 0.2.1 adds several functions.
- avg_alpha – Calculates Shannon, Observed, Pielou, Simpson and Inverse Simpson alpha-diversity metrics as the mean or median of repetitive samplings of the OTU table.
- check_primer_hits – Determines hits of all orientations of the primers to paired sequence files. Used to determine if merging will create overhangs.
- format_taxon – Adds *’s around proper parts of taxon names so that the names can be rendered in italics by Rmarkdown. Useful in making ggplots.
- hash_dna_seqs – Converts DNA seequences into hashes encoding the sequences. Useful in shortening the taxa names especially when using the R verision of DADA2 which outputs the OTU column names as the sequences themselves.
- plot_transition_stats – Makes a plot of DADA2 transition rates from the transition stats qza file output by QIIME2 DADA2 beginning with QIIME 2 version 2025.7. Useful in determing how well DADA2 corrected sequence errors.
- se – calculates the standard eror.
- %wo% – given vectors x and y, returns elements of x that are not in y.