\code{archR} 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. \code{archR} 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. \code{archR} 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.
Package details |
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Bioconductor views | Clustering DNASeq DimensionReduction FeatureExtraction GeneRegulation Genetics MathematicalBiology MotifDiscovery SystemsBiology Transcriptomics |
Maintainer | |
License | GPL-3 | file LICENSE |
Version | 0.1.8 |
URL | https://snikumbh.github.io/archR/ https://github.com/snikumbh/archR |
Package repository | View on GitHub |
Installation |
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