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coil
View on CRAN: Click
here
Download and install coil package within the R console
Install from CRAN:
install.packages("coil")
Install from Github:
library("remotes")
install_github("cran/coil")
Install by package version:
library("remotes")
install_version("coil", "1.2.4")
Attach the package and use:
library("coil")
Maintained by
Cameron M. Nugent
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
First Published: 2019-10-09
Latest Update: 2024-01-11
Description:
Designed for the cleaning, contextualization and assessment of cytochrome c
oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains
functions for placing COI-5P barcode sequences into a common reading frame,
translating DNA sequences to amino acids and for assessing the likelihood that a
given barcode sequence includes an insertion or deletion error. The error assessment
relies on the comparison of input sequences against nucleotide and amino acid profile
hidden Markov models (PHMMs) (for details see Durbin et al. 1998, ISBN: 9780521629713)
trained on a taxonomically diverse set of reference sequences. The functions are
provided as a complete pipeline and are also available individually for efficient and
targeted analysis of barcode data.
How to cite:
Cameron M. Nugent (2019). coil: Contextualization and Evaluation of COI-5P Barcode Data. R package version 1.2.4, https://cran.r-project.org/web/packages/coil. Accessed 06 May. 2025.
Previous versions and publish date:
Other packages that cited coil R package
View coil citation profile
Other R packages that coil depends,
imports, suggests or enhances
Complete documentation for coil
Functions, R codes and Examples using
the coil R package
Some associated functions: aa_coi_PHMM . censored_translation . coi5p . coi5p_pipe . coil . example_barcode_data . example_nt_string . flatten_coi5p . frame . indel_check . individual_AAbin . individual_DNAbin . ins_front_trim . leading_ins . new_coi5p . nt_coi_PHMM . print.coi5p . set_frame . subsetPHMM . trans_df . translate . translate_codon . validate_coi5p . which_trans_table .
Some associated R codes: Full coil package functions and examples
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