Working with Metabarcoding Data in a Tidy Format

Documentation for package ‘eDNAfuns’ version 0.1.0

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AMPURE	AMPURE
ASV_table	ASV_table
count_stop_codons	Count stop codons or return translated sequence
eDNAindex	Create scaled relative proportions of the number of reads of taxa in different samples
example_hashes	example_hashes
fasta_reader	Read FASTA or FASTQ files into a tibble
fasta_writer	Read FASTA or FASTQ files into a tibble
fastq_reader	Read FASTA or FASTQ files into a tibble
fastq_writer	Read FASTA or FASTQ files into a tibble
Index_PCR	Index_PCR
metadata	metadata
molarity.data	molarity.data
mutation	Generate mutated DNA sequences
ng2nM	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/mul for mass nM for molarity
nM2ng	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/mul for mass nM for molarity
OTU_taxonomy	OTU_taxonomy
phyloseq2tidy	Convert a tidy ASV table to a phyloseq object
plot_seq_len_hist	Plot sequence length distribution
ps	ps
read_indexing_PCR	Read Indexing PCR Spreadsheet
read_info_file	Read cutadapt info files
read_step1_PCR	Read Indexing PCR Spreadsheet
tally_wide	Create contingency tables with two variables
template_PCR	template_PCR
test_seqs	test_seqs
tibble_to_comm	Convert a long tibble to a community matrix
tibble_to_dist	Convert a long tibble to a community matrix
tibble_to_env	Convert a long tibble to a community matrix
tidy2phyloseq	Convert a tidy ASV table to a phyloseq object
training.ASV.table	training.ASV.table
training.metadata	training.metadata
tree	tree
UDI_Indices	UDI_Indices
write_indexing_PCR	Write Indexing PCR Spreadsheet