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
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see odseq.
Outlier detection in multiple sequence alignments
Bioconductor version: 3.3
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")
| R Script | A quick tutorial to outlier detection in MSAs | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Alignment, MultipleSequenceAlignment, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| 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.
| Package Source | odseq_1.0.2.tar.gz |
| Windows Binary | odseq_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | odseq_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/odseq/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/odseq/ |
| Package Downloads Report | Download Stats |
Documentation »
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