seqPattern

This package is for version 3.20 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: 3.20

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 "4.4") and enter:


if (!require("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")

seqPattern PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews SequenceMatching, Software, Visualization

Version 1.38.0

In Bioconductor since BioC 3.1 (R-3.2) (10 years)

License GPL-3

Depends methods, R (>= 2.15.0)

Imports Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix

System Requirements

URL

Suggests BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle

Linking To

Enhances parallel

Depends On Me

Imports Me genomation, seqArchRplus

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package seqPattern_1.38.0.tar.gz

Windows Binary (x86_64) seqPattern_1.38.0.zip

macOS Binary (x86_64) seqPattern_1.38.0.tgz

macOS Binary (arm64) seqPattern_1.38.0.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/

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