Type: Package
Package: seqArchR
Title: Identify Different Architectures of Sequence Elements
Version: 1.12.0
Authors@R: 
    person("Sarvesh", "Nikumbh", 
    email = "sarvesh.nikumbh@gmail.com", 
    role = c("aut", "cre", "cph"), 
    comment = c(ORCID = "0000-0003-3163-4447"))
Description: 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.
License: GPL-3 | file LICENSE
URL: https://snikumbh.github.io/seqArchR/,
        https://github.com/snikumbh/seqArchR
BugReports: https://github.com/snikumbh/seqArchR/issues
SystemRequirements: Python (>= 3.5), scikit-learn (>= 0.21.2),
        packaging
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)
Suggests: cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22),
        rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>=
        0.3.0)
VignetteBuilder: knitr
biocViews: MotifDiscovery, GeneRegulation, MathematicalBiology,
        SystemsBiology, Transcriptomics, Genetics, Clustering,
        DimensionReduction, FeatureExtraction, DNASeq
Encoding: UTF-8
RoxygenNote: 7.2.1
git_url: https://git.bioconductor.org/packages/seqArchR
git_branch: RELEASE_3_21
git_last_commit: 686a521
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-28
NeedsCompilation: no
Packaged: 2025-04-29 05:54:08 UTC; biocbuild
Author: Sarvesh Nikumbh [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-3163-4447>)
Maintainer: Sarvesh Nikumbh <sarvesh.nikumbh@gmail.com>
Built: R 4.5.0; ; 2025-04-29 21:22:41 UTC; unix
