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debar
View on CRAN: Click
here
Download and install debar package within the R console
Install from CRAN:
install.packages("debar")
Install from Github:
library("remotes")
install_github("cran/debar")
Install by package version:
library("remotes")
install_version("debar", "0.1.1")
Attach the package and use:
library("debar")
Maintained by
Cameron M. Nugent
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-12-22
Latest Update: 2024-01-12
Description:
The 'debar' sequence processing pipeline is designed for denoising high throughput
sequencing data for the animal DNA barcode marker cytochrome c oxidase I (COI). The package
is designed to detect and correct insertion and deletion errors within sequencer outputs.
This is accomplished through comparison of input sequences against a profile hidden Markov
model (PHMM) using the Viterbi algorithm (for algorithm details see Durbin et al. 1998,
ISBN: 9780521629713). Inserted base pairs are removed and deleted base pairs are accounted
for through the introduction of a placeholder character. Since the PHMM is a probabilistic
representation of the COI barcode, corrections are not always perfect. For this reason
'debar' censors base pairs adjacent to reported indel sites, turning them into placeholder
characters (default is 7 base pairs in either direction, this feature can be disabled).
Testing has shown that this censorship results in the correct sequence length being restored,
and erroneous base pairs being masked the vast majority of the time (>95%).
How to cite:
Cameron M. Nugent (2019). debar: A Post-Clustering Denoiser for COI-5P Barcode Data. R package version 0.1.1, https://cran.r-project.org/web/packages/debar. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1.0 (2019-12-22 16:50)
Other packages that cited debar R package
View debar citation profile
Other R packages that debar depends,
imports, suggests or enhances
Complete documentation for debar
Functions, R codes and Examples using
the debar R package
Some associated functions: DNAseq . aa_check . adj_seq . adjust . censored_translation . col_mode . consensus . debar . denoise . denoise_file . denoise_list . dir_check . ex_nt_list . example_nt_string . example_nt_string_errors . frame . individual_DNAbin . ins_front_trim . leading_ins . meta_check . new_DNAseq . nt_PHMM . outseq . print.DNAseq . read_fasta . read_fastq . rev_comp . set_frame . translate_codon . triple_dels . triple_ins . validate_DNAseq . write_fasta . write_fastq . write_wrapper .
Some associated R codes: Full debar package functions and examples
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