Package: PscanR
Type: Package
Title: Motif Enrichment Analysis of Regulatory DNA Sequences
Version: 0.99.4
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,
        PscanRBackgrounds, 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"),
    person("Italy's National Recovery and Resilience Plan (PNRR)",
        role = "fnd", comment = "project ELIXIRNextGenIT, R0000010"))
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
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://bioc.r-universe.dev
Date/Publication: 2026-11-11 13:29:05 UTC
RemoteUrl: https://github.com/bioc/PscanR
RemoteRef: HEAD
RemoteSha: be6299a2f0d99fc71faa7e4d58161b7851cdd53c
NeedsCompilation: no
Packaged: 2026-11-11 22:18:20 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],
  Italy's National Recovery and Resilience Plan (PNRR) [fnd] (project
    ELIXIRNextGenIT, R0000010)
Maintainer: Federico Zambelli <federico.zambelli@unimi.it>