seqArchR

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

Identify Different Architectures of Sequence Elements


Bioconductor version: Development (3.21)

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: )

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")

# 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

Reference Manual PDF

Details

biocViews Clustering, DNASeq, DimensionReduction, FeatureExtraction, GeneRegulation, Genetics, MathematicalBiology, MotifDiscovery, Software, SystemsBiology, Transcriptomics
Version 1.11.0
In Bioconductor since BioC 3.15 (R-4.2) (2.5 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
See More
Suggests cowplot, hopach(>= 2.42.0), BiocStyle, knitr (>= 1.22), rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>= 0.3.0)
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Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/seqArchR/
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