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seqPattern

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

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

Bioconductor version: Development (3.18)

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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
seqPattern PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews SequenceMatching, Software, Visualization
Version 1.33.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL-3
Depends methods, R (>= 2.15.0)
Imports Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
Linking To
Suggests BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle
System Requirements
Enhances parallel
URL
See More
Depends On Me
Imports Me genomation, seqArchRplus
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package seqPattern_1.33.0.tar.gz
Windows Binary seqPattern_1.33.0.zip
macOS Binary (x86_64) seqPattern_1.33.0.tgz
macOS Binary (arm64) seqPattern_1.33.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/seqPattern
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seqPattern
Bioc Package Browser https://code.bioconductor.org/browse/seqPattern/
Package Short Url https://bioconductor.org/packages/seqPattern/
Package Downloads Report Download Stats