seqArchR
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see seqArchR.
Identify Different Architectures of Sequence Elements
Bioconductor version: 3.15
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("seqArchR")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DNASeq, DimensionReduction, FeatureExtraction, GeneRegulation, Genetics, MathematicalBiology, MotifDiscovery, Software, SystemsBiology, Transcriptomics |
| Version | 1.0.0 |
| 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) |
| 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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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | seqArchR_1.0.0.tar.gz |
| Windows Binary | seqArchR_1.0.0.zip |
| macOS Binary (x86_64) | seqArchR_1.0.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.15 | Source Archive |