Package: PscanR
Type: Package
Title: Motif Enrichment Analysis of Regulatory DNA Sequences
Version: 0.99.0
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: BiocFileCache, BiocParallel, BiocGenerics, Biostrings,
        ExperimentHub, ggplot2, grDevices, methods, pheatmap, RSQLite,
        stats, TFBSTools, UCSC.utils, utils
Suggests: AnnotationDbi, BiocStyle, BSgenome,
        BSgenome.Athaliana.TAIR.TAIR9, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Mmusculus.UCSC.mm10,
        BSgenome.Scerevisiae.UCSC.sacCer3, GenomicFeatures,
        GenomicRanges, GenomeInfoDb, IRanges, JASPAR2020, JASPAR2022,
        JASPAR2024, knitr, org.Hs.eg.db, org.Mm.eg.db, org.Sc.sgd.db,
        rmarkdown, testthat, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
        txdbmaker
biocViews: SequenceMatching, Transcription, GeneRegulation,
        MotifAnnotation
Authors@R: c(person("Federico", "Zambelli", email = "federico.zambelli@unimi.it", 
    role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3487-4331")),
    person("Giulio", "Pavesi", email = "giulio.pavesi@unimi.it", role = "aut",
    comment = c(ORCID = "0000-0001-5705-6249")),
    person("Diana", "Betelli", role = "ctb"))
Description: R implementation of the 'Pscan' algorithm for motif
        enrichment analysis in regulatory DNA sequences, based on
        Zambelli et al. (2009) <doi:10.1093/nar/gkp464>. 'PscanR' scans
        a set of DNA sequences (e.g., promoters) from co-regulated or
        co-expressed genes, using transcription factor binding motifs
        from databases such as JASPAR. It identifies significantly
        enriched motifs, providing thus hints on which transcription
        factors could be common regulators of the genes studied,
        together with the location of their candidate binding sites in
        the sequences.
License: GPL-3
VignetteBuilder: knitr
URL: https://github.com/Federico77z/PscanR
BugReports: https://github.com/Federico77z/PscanR/issues
RoxygenNote: 8.0.0
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: make libgsl0-dev libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-10-06 11:25:03 UTC
RemoteUrl: https://github.com/BiocStaging/PscanR
RemoteRef: HEAD
RemoteSha: 3d1af59dabb6a6a293d418468919fc07368c08f9
NeedsCompilation: no
Packaged: 2026-10-07 08:32:09 UTC; root
Author: Federico Zambelli [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3487-4331>),
  Giulio Pavesi [aut] (ORCID: <https://orcid.org/0000-0001-5705-6249>),
  Diana Betelli [ctb]
Maintainer: Federico Zambelli <federico.zambelli@unimi.it>