To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("odseq")

In most cases, you don't need to download the package archive at all.

odseq

DOI: 10.18129/B9.bioc.odseq    

This is the development version of odseq; for the stable release version, see odseq.

Outlier detection in multiple sequence alignments

Bioconductor version: Development (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("odseq")

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 1.5.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 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
Suggests Me
Build Report  

Package Archives

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

Source Package odseq_1.5.0.tar.gz
Windows Binary odseq_1.5.0.zip
Mac OS X 10.11 (El Capitan) odseq_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/odseq
Package Short Url http://bioconductor.org/packages/odseq/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: