Package: PscanR
Type: Package
Title: Motif Enrichment Analysis of Regulatory DNA Sequences
Version: 0.99.4
Encoding: UTF-8
Depends: R (>= 4.6.0)
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
git_url: https://git.bioconductor.org/packages/PscanR
git_branch: devel
git_last_commit: be6299a
git_last_commit_date: 2026-11-11
Repository: Bioconductor 3.24
Date/Publication: 2026-11-11
NeedsCompilation: no
Packaged: 2026-11-12 01:03:33 UTC; biocbuild
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>
