Package: insect 1.4.4

insect: Informatic Sequence Classification Trees

Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.

Authors:Shaun Wilkinson [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
insect/json (API)

# Install 'insect' in R:

install.packages('insect', repos = c('https://shaunpwilkinson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/shaunpwilkinson/insect/issues

Datasets:

samoa - Table of marine COI amplicon sequence variants from American Samoa
whale_taxonomy - Cetacean section of NCBI taxonomy database.
whales - Cetacean 16S rDNA sequences.

On CRAN:

6.72 score 15 stars 2 packages 117 scripts 893 downloads 1 mentions 39 exports 24 dependencies

Last updated from:6917b45387. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	153
source / vignettes	OK	202
linux-release-x86_64	OK	145
macos-release-arm64	OK	89
macos-oldrel-arm64	OK	108
windows-devel	OK	198
windows-release	OK	151
windows-oldrel	OK	107
wasm-release	OK	130

Exports:aa2char allocateCVI char2aa char2dna classify decodePHMM demultiplex dereplicate disambiguate dna2char duplicated.AAbin duplicated.DNAbin encodePHMM expand get_lineage get_taxID hash join learn prune_taxonomy purge qfilter rc readFASTA readFASTQ rereplicate searchGB shave stitch subset.AAbin subset.DNAbin taxonomy trim unique.AAbin unique.DNAbin virtualFISH virtualPCR writeFASTA writeFASTQ

Dependencies:ade4 ape aphid askpass cli curl digest kmer lattice MASS nlme openssl phylogram pixmap qpdf RANN Rcpp RcppArmadillo rlang segmented seqinr sp sys xml2

The insect R package

Rendered frominsect-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-05-24
Started: 2018-03-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Allocate sequences for cross validation by identity.	allocateCVI
Tree-based sequence classification.	classify
Convert sequences between binary and character string formats.	aa2char char2aa char2dna conversion dna2char
Demultiplex merged FASTQ	demultiplex
Convert oligonucleotide sequences into regular expressions.	disambiguate
Encode and decode profile HMMs in raw byte format.	decodePHMM encodePHMM encoding
Expand an existing classification tree.	expand
Get full lineage details from a taxonomic ID number.	get_lineage
Get taxon ID from taxonomy database.	get_taxID
Convert sequences to MD5 hashes.	hash
Informatic sequence classification trees.	insect-package insect
Concatenate DNAbin objects while preserving attributes.	join
Informatic sequence classification tree learning.	learn
Further bit-level manipulation of DNA and amino acid sequences.	duplicated.AAbin duplicated.DNAbin manipulate subset.AAbin subset.DNAbin unique.AAbin unique.DNAbin
Prune taxonomy database.	prune_taxonomy
Identify and remove erroneous reference sequences.	purge
Quality filtering for amplicon sequences.	qfilter
Reverse complement DNA in character string format.	rc
Read FASTA and FASTQ files.	read readFASTA readFASTQ
Dereplicate and rereplicate sequence datasets.	dereplicate replicate rereplicate
Table of marine COI amplicon sequence variants from American Samoa	samoa
Query the NCBI GenBank database.	searchGB
Shave ends from DNA and amino acid sequences	shave
Paired-end read stitching.	stitch
Download taxonomy database.	taxonomy
Trim primer and/or index sequences.	trim
Virtual _in situ_ hybridization.	virtualFISH
Virtual PCR.	virtualPCR
Cetacean section of NCBI taxonomy database.	whale_taxonomy
Cetacean 16S rDNA sequences.	whales
Write sequences to text in FASTA or FASTQ format.	write writeFASTA writeFASTQ