Type: Package
Package: seqArchRplus
Title: Downstream analyses of promoter sequence architectures and HTML
        report generation
Version: 1.10.0
Authors@R: 
    person("Sarvesh", "Nikumbh", , "sarvesh.nikumbh@gmail.com", 
    role = c("aut", "cre", "cph"),
    comment = c(ORCID = "0000-0003-3163-4447"))
Description: seqArchRplus facilitates downstream analyses of promoter
        sequence architectures/clusters identified by seqArchR (or any
        other tool/method). With additional available information such
        as the TPM values and interquantile widths (IQWs) of the CAGE
        tag clusters, seqArchRplus can order the input promoter
        clusters by their shape (IQWs), and write the cluster
        information as browser/IGV track files. Provided visualizations
        are of two kind: per sample/stage and per cluster
        visualizations. Those of the first kind include: plot panels
        for each sample showing per cluster shape, TPM and other score
        distributions, sequence logos, and peak annotations. The second
        include per cluster chromosome-wise and strand distributions,
        motif occurrence heatmaps and GO term enrichments.
        Additionally, seqArchRplus can also generate HTML reports for
        easy viewing and comparison of promoter architectures between
        samples/stages.
License: GPL-3
URL: https://github.com/snikumbh/seqArchRplus
BugReports: https://github.com/snikumbh/seqArchRplus/issues
Depends: R (>= 4.2), GenomicRanges, IRanges, S4Vectors
Imports: BiocParallel, Biostrings, BSgenome, ChIPseeker, cli,
        clusterProfiler, cowplot, factoextra, Seqinfo, ggplot2,
        ggimage, graphics, grDevices, gridExtra, heatmaps, magick,
        methods, RColorBrewer, scales, seqArchR, seqPattern, stats,
        utils
Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2),
        covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>=
        1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun
VignetteBuilder: knitr
biocViews: Annotation, Visualization, ReportWriting, GO,
        MotifAnnotation, Clustering
Encoding: UTF-8
RoxygenNote: 7.2.3
PackageStatus: Deprecated
Config/pak/sysreqs: libcairo2-dev cmake libfftw3-dev libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libmagick++-dev gsfonts
        libbz2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev
        libtiff-dev libxml2-dev libssl-dev python3 xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:20:15 UTC
RemoteUrl: https://github.com/bioc/seqArchRplus
RemoteRef: RELEASE_3_22
RemoteSha: 7ad13f0450eb9cc5abbffc00e5bc984a8f73e822
NeedsCompilation: no
Packaged: 2025-12-24 08:35:17 UTC; root
Author: Sarvesh Nikumbh [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-3163-4447>)
Maintainer: Sarvesh Nikumbh <sarvesh.nikumbh@gmail.com>
Built: R 4.5.2; ; 2025-12-24 08:52:26 UTC; unix
