seqArchR

DOI: 10.18129/B9.bioc.seqArchR    

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

Identify Different Architectures of Sequence Elements

Bioconductor version: Development (3.16)

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 "4.2") 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")

 

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 1.1.0
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
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)
Enhances
URL https://snikumbh.github.io/seqArchR/ https://github.com/snikumbh/seqArchR
BugReports https://github.com/snikumbh/seqArchR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package seqArchR_1.1.0.tar.gz
Windows Binary seqArchR_1.1.1.zip
macOS Binary (x86_64) seqArchR_1.1.1.tgz
macOS Binary (arm64) seqArchR_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/seqArchR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seqArchR
Package Short Url https://bioconductor.org/packages/seqArchR/
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