Package: insect 1.4.0.9000

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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insect.pdf |insect.html✨
insect/json (API)

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

Peer review:

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:

5.76 score 14 stars 82 scripts 731 downloads 1 mentions 39 exports 22 dependencies

Last updated 3 years agofrom:8be355c61a. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winNOTENov 04 2024
R-4.5-linuxNOTENov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024
R-4.3-winOKNov 04 2024
R-4.3-macOKNov 04 2024

Exports:aa2charallocateCVIchar2aachar2dnaclassifydecodePHMMdemultiplexdereplicatedisambiguatedna2charduplicated.AAbinduplicated.DNAbinencodePHMMexpandget_lineageget_taxIDhashjoinlearnprune_taxonomypurgeqfilterrcreadFASTAreadFASTQrereplicatesearchGBshavestitchsubset.AAbinsubset.DNAbintaxonomytrimunique.AAbinunique.DNAbinvirtualFISHvirtualPCRwriteFASTAwriteFASTQ

Dependencies:ade4apeaphidaskpassclidigestkmerlatticeMASSnlmeopensslphylogrampixmapRANNRcppRcppArmadillorlangsegmentedseqinrspsysxml2

The insect R package

Rendered frominsect-vignette.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2018-12-22
Started: 2018-03-08

Readme and manuals

Help Manual

Help pageTopics
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 FASTQdemultiplex
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
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 Samoasamoa
Query the NCBI GenBank database.searchGB
Shave ends from DNA and amino acid sequencesshave
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