Working with Metabarcoding Data in a Tidy Format
Count stop codons or return translated sequence
Create scaled relative proportions of the number of reads of taxa in d...
Read FASTA or FASTQ files into a tibble
Read FASTA or FASTQ files into a tibble
Generate mutated DNA sequences
functions to translate mass into molarity and vice versa, given we are...
Convert a tidy ASV table to a phyloseq object
Plot sequence length distribution
Read cutadapt info files
Read Indexing PCR Spreadsheet
Create contingency tables with two variables
Convert a long tibble to a community matrix
Write Indexing PCR Spreadsheet
A series of R functions that come in handy while working with metabarcoding data. 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' from Wickham et al.(2019) <doi:10.21105/joss.01686> with the functions we have used in community ecology compiled in packages like 'vegan' from Dixon (2003) <doi:10.1111/j.1654-1103.2003.tb02228.x> and 'phyloseq' McMurdie & Holmes (2013) <doi:10.1371/journal.pone.0061217>. The package includes functions to read sequences from FAST(A/Q) into a tibble ('fasta_reader' and 'fastq_reader'), to process 'cutadapt' Martin (2011) <doi:10.14806/ej.17.1.200> 'info-file' output. When it comes to sequence counts across samples, the package works with the long format in mind (a three column 'tibble' with Sample, Sequence and counts ), with functions to move from there to the wider format.