R: Working with Metabarcoding Data in a Tidy Format

# Working with Metabarcoding Data in a Tidy Format

## Documentation for package ‘eDNAfuns’ version 0.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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