odseq

DOI: 10.18129/B9.bioc.odseq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see odseq.

Outlier detection in multiple sequence alignments

Bioconductor version: 3.9

Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for aligned sequences and a variant using string kernels for unaligned sequences.

Author: José Jiménez

Maintainer: José Jiménez <jose at jimenezluna.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("odseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("odseq")

 

PDF	R Script	A quick tutorial to outlier detection in MSAs
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Alignment, MultipleSequenceAlignment, Software
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.2.3)
Imports	msa(>= 1.2.1), kebabs(>= 1.4.1), mclust (>= 5.1)
LinkingTo
Suggests	knitr (>= 1.11)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	odseq_1.12.0.tar.gz
Windows Binary	odseq_1.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	odseq_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/odseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/odseq
Package Short Url	https://bioconductor.org/packages/odseq/
Package Downloads Report	Download Stats