This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

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>

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

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

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)
Linking To
Suggests cowplot, hopach(>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0)
System Requirements Python (>= 3.5), scikit-learn (>= 0.21.2), packaging
Enhances
URL https://snikumbh.github.io/seqArchR/ https://github.com/snikumbh/seqArchR
Bug Reports https://github.com/snikumbh/seqArchR/issues
See More
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