Type: Package
Package: seqArchRplus
Title: Downstream analyses of promoter sequence architectures and HTML
        report generation
Version: 1.2.0
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, GenomeInfoDb, 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
git_url: https://git.bioconductor.org/packages/seqArchRplus
git_branch: RELEASE_3_18
git_last_commit: ce8bb37
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: no
Packaged: 2023-10-24 23:03:59 UTC; biocbuild
Author: Sarvesh Nikumbh [aut, cre, cph]
    (<https://orcid.org/0000-0003-3163-4447>)
Maintainer: Sarvesh Nikumbh <sarvesh.nikumbh@gmail.com>
Built: R 4.3.2; ; 2023-12-12 10:37:30 UTC; unix
