This is the development version of seqArchR; for the stable release version, see seqArchR.
Identify Different Architectures of Sequence ElementsBioconductor version: Development (3.22)
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] ORCID: 0000-0003-3163-4447
Maintainer: Sarvesh Nikumbh <sarvesh.nikumbh at gmail.com>
Citation (from within R, entercitation("seqArchR")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("seqArchR")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("seqArchR")Follow Installation instructions to use this package in your R session.
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