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odseq

Outlier detection in multiple sequence alignments


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("odseq")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
A quick tutorial to outlier detection in MSAs PDF R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Alignment, MultipleSequenceAlignment, Software
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License MIT + file LICENSE
Depends R (>= 3.2.3)
Imports msa(>= 1.2.1), kebabs(>= 1.4.1), mclust (>= 5.1)
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Suggests knitr (>= 1.11)
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Package Archives

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

Source Package odseq_1.30.0.tar.gz
Windows Binary odseq_1.30.0.zip (64-bit only)
macOS Binary (x86_64) odseq_1.30.0.tgz
macOS Binary (arm64) odseq_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/odseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/odseq
Bioc Package Browser https://code.bioconductor.org/browse/odseq/
Package Short Url https://bioconductor.org/packages/odseq/
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