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>
citation("odseq")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Alignment, MultipleSequenceAlignment, Software |
| Version | 1.12.0 |
| 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) |
| System Requirements | |
| URL |
See More
| Suggests | knitr (>= 1.11) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/odseq/ |
| Package Short Url | https://bioconductor.org/packages/odseq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |