seqPattern

DOI: 10.18129/B9.bioc.seqPattern    

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

Visualising oligonucleotide patterns and motif occurrences across a set of sorted sequences

Bioconductor version: 3.9

Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

Author: Vanja Haberle <vanja.haberle at gmail.com>

Maintainer: Vanja Haberle <vanja.haberle at gmail.com>

Installation

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

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

BiocManager::install("seqPattern")

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("seqPattern")

 

PDF	R Script	seqPattern
PDF		Reference Manual
Text		NEWS

Details

biocViews	SequenceMatching, Software, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (4.5 years)
License	GPL-3
Depends	methods, R (>= 2.15.0)
Imports	Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
LinkingTo
Suggests	BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle
SystemRequirements
Enhances	parallel
URL
Depends On Me
Imports Me	genomation
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	seqPattern_1.16.0.tar.gz
Windows Binary	seqPattern_1.16.0.zip
Mac OS X 10.11 (El Capitan)	seqPattern_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seqPattern
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqPattern
Package Short Url	https://bioconductor.org/packages/seqPattern/
Package Downloads Report	Download Stats