seqArchR

This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see seqArchRplus.

Identify Different Architectures of Sequence Elements

DOI: 10.18129/B9.bioc.seqArchR

Bioconductor version: 3.21

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 iD ORCID: 0000-0003-3163-4447

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, DNASeq, DimensionReduction, FeatureExtraction, GeneRegulation, Genetics, MathematicalBiology, MotifDiscovery, Software, SystemsBiology, Transcriptomics

Version 1.12.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 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)

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

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_1.12.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) seqArchR_1.12.0.tgz

macOS Binary (arm64) seqArchR_1.12.0.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/

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