seqArchR

DOI: 10.18129/B9.bioc.seqArchR  

Identify Different Architectures of Sequence Elements

Bioconductor version: Release (3.17)

seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.

Author: Sarvesh Nikumbh [aut, cre, cph]

Maintainer: Sarvesh Nikumbh <sarvesh.nikumbh at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("seqArchR")

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("seqArchR")

 

HTML	R Script	Example usage of _seqArchR_ on simulated DNA sequences
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, DNASeq, DimensionReduction, FeatureExtraction, GeneRegulation, Genetics, MathematicalBiology, MotifDiscovery, Software, SystemsBiology, Transcriptomics
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3 | file LICENSE
Depends	R (>= 4.2.0)
Imports	utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods, stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2 (>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings, grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1)
LinkingTo
Suggests	cowplot, hopach(>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0)
SystemRequirements	Python (>= 3.5), scikit-learn (>= 0.21.2), packaging
Enhances
URL	https://snikumbh.github.io/seqArchR/ https://github.com/snikumbh/seqArchR
BugReports	https://github.com/snikumbh/seqArchR/issues
Depends On Me
Imports Me	seqArchRplus
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	seqArchR_1.4.0.tar.gz
Windows Binary	seqArchR_1.4.0.zip
macOS Binary (x86_64)	seqArchR_1.4.0.tgz
macOS Binary (arm64)	seqArchR_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seqArchR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqArchR
Bioc Package Browser	https://code.bioconductor.org/browse/seqArchR/
Package Short Url	https://bioconductor.org/packages/seqArchR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive