eDNAfuns
Working with Metabarcoding Data in a Tidy Format
Description
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.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | ERROR |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
package dependencies
Packages required but not available: 'phyloseq', 'Biostrings' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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Check History
ERROR 12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 9, 2026
package dependencies
Packages required but not available: 'phyloseq', 'Biostrings' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘phyloseq’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.