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>

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

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

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