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eDNA_functions

A series of R functions that come in handy while working with metabarcoding data. Made by Ramon Gallego while working at the Kelly Lab (). The reasoning of doing this is to have the same functions we use all the time stored in a curated, reproducible way. In a way it is all about putting together the grammar of the tidyverse with the functions we have used in community ecology.

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Version

Install

install.packages('eDNAfuns')

Monthly Downloads

151

Version

0.1.0

License

GPL (>= 3)

Maintainer

Ramón Gallego Simón

Last Published

October 1st, 2025

Functions in eDNAfuns (0.1.0)

write_indexing_PCR

Write Indexing PCR Spreadsheet

training.ASV.table

training.ASV.table

Convert a long tibble to a community matrix

Read cutadapt info files

Create contingency tables with two variables

training.metadata

training.metadata

Create scaled relative proportions of the number of reads of taxa in different samples

Read FASTA or FASTQ files into a tibble

Read FASTA or FASTQ files into a tibble

count_stop_codons

Count stop codons or return translated sequence

read_indexing_PCR

Read Indexing PCR Spreadsheet

Convert a tidy ASV table to a phyloseq object

Generate mutated DNA sequences

functions to translate mass into molarity and vice versa, given we are talking about double stranded DNA it requires two inputs, the mass (or molarity) and the length of the DNA fragment It works with the two most common concentrations used in Molecular Ecology labs ng/\(\mu\)l for mass nM for molarity

plot_seq_len_hist

Plot sequence length distribution