UDI_Indices

Placeholder description for UDI_Indices dataset.

datasets

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.

Ramón Gallego Simón

eDNAfuns

Working with Metabarcoding Data in a Tidy Format

UDI_Indices function

A data frame with 384 rows and 6 columns<dl>
 <dt>Index</dt>
<dd>Character vector</dd> <dt>Bases_in_Adapter_i7</dt>
<dd>Seqs in i7</dd> <dt>Bases_for_Sample_Sheet_i7</dt>
<dd>Seqs to include</dd> <dt>Bases_for_Sample_Sheet_i5</dt>
<dd>Seqs to include in some illumina platoforms</dd> <dt>Bases_for_Sample_Sheet_i5_B</dt>
<dd>Seqs to include in other illumina platoforms</dd> <dt>Set</dt>
<dd>A, B, C, or D</dd>
</dl>

Format

UDI_Indices — UDI_Indices

A data frame with 384 rows and 6 columns<dl>
 <dt>Index</dt>
<dd>Character vector</dd>

 <dt>Bases_in_Adapter_i7</dt>
<dd>Seqs in i7</dd>

 <dt>Bases_for_Sample_Sheet_i7</dt>
<dd>Seqs to include</dd>

 <dt>Bases_for_Sample_Sheet_i5</dt>
<dd>Seqs to include in some illumina platoforms</dd>

 <dt>Bases_for_Sample_Sheet_i5_B</dt>
<dd>Seqs to include in other illumina platoforms</dd>

 <dt>Set</dt>
<dd>A, B, C, or D</dd>


</dl>

UDI_Indices: UDI_Indices

Description

Usage

Arguments

Format