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seqArchR

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

Identify Different Architectures of Sequence Elements


Bioconductor version: Development (3.19)

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 "4.4") 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.

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

Details

biocViews Clustering, DNASeq, DimensionReduction, FeatureExtraction, GeneRegulation, Genetics, MathematicalBiology, MotifDiscovery, Software, SystemsBiology, Transcriptomics
Version 1.7.0
In Bioconductor since BioC 3.15 (R-4.2) (2 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)
System Requirements Python (>= 3.5), scikit-learn (>= 0.21.2), packaging
URL https://snikumbh.github.io/seqArchR/ https://github.com/snikumbh/seqArchR
Bug Reports https://github.com/snikumbh/seqArchR/issues
See More
Suggests cowplot, hopach(>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0)
Linking To
Enhances
Depends On Me
Imports Me seqArchRplus
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Package Archives

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

Source Package seqArchR_1.7.0.tar.gz
Windows Binary
macOS Binary (x86_64) seqArchR_1.7.0.tgz
macOS Binary (arm64)
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