{
  "_id": "6ac61506f511ae58c09a5bb0",
  "Package": "PscanR",
  "Type": "Package",
  "Title": "Motif Enrichment Analysis of Regulatory DNA Sequences",
  "Version": "0.99.0",
  "Encoding": "UTF-8",
  "biocViews": "SequenceMatching, Transcription, GeneRegulation,\nMotifAnnotation",
  "Authors@R": "c(person(\"Federico\", \"Zambelli\", email = \"federico.zambelli@unimi.it\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-3487-4331\")),\nperson(\"Giulio\", \"Pavesi\", email = \"giulio.pavesi@unimi.it\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-5705-6249\")),\nperson(\"Diana\", \"Betelli\", role = \"ctb\"))",
  "Description": "R implementation of the 'Pscan' algorithm for motif\nenrichment analysis in regulatory DNA sequences, based on\nZambelli et al. (2009) <doi:10.1093/nar/gkp464>. 'PscanR' scans\na set of DNA sequences (e.g., promoters) from co-regulated or\nco-expressed genes, using transcription factor binding motifs\nfrom databases such as JASPAR. It identifies significantly\nenriched motifs, providing thus hints on which transcription\nfactors could be common regulators of the genes studied,\ntogether with the location of their candidate binding sites in\nthe 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",
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  "Config/pak/sysreqs": "make libgsl0-dev libbz2-dev libicu-dev liblzma-dev\nlibpng-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": {
    "Date": "2026-10-07 08:32:09 UTC",
    "User": "root"
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  "Author": "Federico Zambelli [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3487-4331>),\nGiulio Pavesi [aut] (ORCID: <https://orcid.org/0000-0001-5705-6249>),\nDiana Betelli [ctb]",
  "Maintainer": "Federico Zambelli <federico.zambelli@unimi.it>",
  "_user": "biocstaging",
  "_type": "src",
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  "_expires": "2027-01-15T09:46:43.000Z",
  "_created": "2026-10-07T08:32:09.000Z",
  "_published": "2026-10-07T16:52:44.411Z",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37593235423",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
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    "note": 1
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  "_upstream": "https://github.com/BiocStaging/PscanR",
  "_commit": {
    "id": "3d1af59dabb6a6a293d418468919fc07368c08f9",
    "author": "Federico77z <36039850+Federico77z@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #83 from Federico77z/Claude\n\nZenodo per-release retrieval; evaluate retrieval in vignettes; fix empty NOTE",
    "time": 1791285903
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  "_maintainer": {
    "name": "Federico Zambelli",
    "email": "federico.zambelli@unimi.it",
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  "_topics": [
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    "transcription",
    "generegulation",
    "motifannotation"
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  "_contributors": [
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      "user": "dianabetelli",
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  },
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    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PscanR"
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  "_devurl": "https://github.com/federico77z/pscanr",
  "_searchresults": 7,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/PscanR.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "ps_available_bg",
    "ps_bg_avg",
    "ps_bg_avg<-",
    "ps_bg_seq_names",
    "ps_bg_size",
    "ps_bg_size<-",
    "ps_bg_std_dev",
    "ps_bg_std_dev<-",
    "ps_build_bg",
    "ps_build_bg_from_table",
    "ps_density_plot",
    "ps_fg_avg",
    "ps_fg_size",
    "ps_get_bg_table",
    "ps_hit_score_plot",
    "ps_hitpos_map",
    "ps_hits_oligo",
    "ps_hits_oligo_bg",
    "ps_hits_pos",
    "ps_hits_pos_bg",
    "ps_hits_score",
    "ps_hits_score_bg",
    "ps_hits_size",
    "ps_hits_strand",
    "ps_hits_strand_bg",
    "ps_hits_table",
    "ps_hits_z",
    "ps_load_select_transcripts",
    "ps_motif_barplot",
    "ps_motif_class",
    "ps_pvalue",
    "ps_results_table",
    "ps_retrieve_bg",
    "ps_retrieve_bg_from_file",
    "ps_scan",
    "ps_select_promoters",
    "ps_selection_summary",
    "ps_seq_names",
    "ps_transcript_legend",
    "ps_write_bg_to_file",
    "ps_z_table",
    "ps_zscore",
    "ps_zscore_heatmap",
    "pscan",
    "pscan_filtered",
    "pscan_full_bg",
    "PSMatrix",
    "PSMatrixList",
    "show"
  ],
  "_help": [
    {
      "page": "ps_available_bg",
      "title": "Get Available Pre-Computed Background Files",
      "topics": [
        "ps_available_bg"
      ]
    },
    {
      "page": "ps_bg_avg",
      "title": "Retrieve the Background Average Score for Motif Enrichment Analysis (Generic Function)",
      "topics": [
        "ps_bg_avg"
      ]
    },
    {
      "page": "ps_bg_avg-PSMatrix-method",
      "title": "Get Background Average Score",
      "topics": [
        "ps_bg_avg,PSMatrix-method"
      ]
    },
    {
      "page": "ps_bg_avg-set",
      "title": "Generic Setter Method for Background Mean Value of an object",
      "topics": [
        "ps_bg_avg<-"
      ]
    },
    {
      "page": "ps_bg_avg-set-PSMatrix-method",
      "title": "Set Background Average",
      "topics": [
        "ps_bg_avg<-,PSMatrix-method"
      ]
    },
    {
      "page": "ps_bg_seq_names",
      "title": "Retrieve Sequence Names for the Background Dataset (Generic Function)",
      "topics": [
        "ps_bg_seq_names"
      ]
    },
    {
      "page": "ps_bg_seq_names-PSMatrix-method",
      "title": "Get Sequence Identifiers of the Background Dataset",
      "topics": [
        "ps_bg_seq_names,PSMatrix-method"
      ]
    },
    {
      "page": "ps_bg_size",
      "title": "Retrieve the Background Size Value for Motif Enrichment Analysis (Generic Function)",
      "topics": [
        "ps_bg_size"
      ]
    },
    {
      "page": "ps_bg_size-PSMatrix-method",
      "title": "Get Background Size",
      "topics": [
        "ps_bg_size,PSMatrix-method"
      ]
    },
    {
      "page": "ps_bg_size-set",
      "title": "Set Background Size (Generic Function)",
      "topics": [
        "ps_bg_size<-"
      ]
    },
    {
      "page": "ps_bg_size-set-PSMatrix-method",
      "title": "Set Background Size in a PSMatrix",
      "topics": [
        "ps_bg_size<-,PSMatrix-method"
      ]
    },
    {
      "page": "ps_bg_std_dev",
      "title": "Retrieve the Background Standard Deviation for Motif Enrichment Analysis (Generic Function)",
      "topics": [
        "ps_bg_std_dev"
      ]
    },
    {
      "page": "ps_bg_std_dev-PSMatrix-method",
      "title": "Get Background Standard Deviation",
      "topics": [
        "ps_bg_std_dev,PSMatrix-method"
      ]
    },
    {
      "page": "ps_bg_std_dev-set",
      "title": "Set Background Standard Deviation (Generic Function)",
      "topics": [
        "ps_bg_std_dev<-"
      ]
    },
    {
      "page": "ps_bg_std_dev-set-PSMatrix-method",
      "title": "Set Background Standard Deviation",
      "topics": [
        "ps_bg_std_dev<-,PSMatrix-method"
      ]
    },
    {
      "page": "ps_build_bg",
      "title": "Build background matrices in parallel",
      "topics": [
        "ps_build_bg"
      ]
    },
    {
      "page": "ps_build_bg_from_table",
      "title": "Apply background parameters to position frequency matrices",
      "topics": [
        "ps_build_bg_from_table"
      ]
    },
    {
      "page": "ps_density_plot",
      "title": "Density Plot of Motif Hits Along Promoter Regions",
      "topics": [
        "ps_density_plot"
      ]
    },
    {
      "page": "ps_fg_avg",
      "title": "Retrieve the Foreground Average Score for Motif Enrichment Analysis (Generic Function)",
      "topics": [
        "ps_fg_avg"
      ]
    },
    {
      "page": "ps_fg_avg-PSMatrix-method",
      "title": "Get Foreground Average Score",
      "topics": [
        "ps_fg_avg,PSMatrix-method"
      ]
    },
    {
      "page": "ps_fg_size",
      "title": "Retrieve the Foreground Size Value for Motif Enrichment Analysis (Generic Function)",
      "topics": [
        "ps_fg_size"
      ]
    },
    {
      "page": "ps_fg_size-PSMatrix-method",
      "title": "Get Foreground Size",
      "topics": [
        "ps_fg_size,PSMatrix-method"
      ]
    },
    {
      "page": "ps_get_bg_table",
      "title": "Extract background statistics from a `PSMatrixList` object",
      "topics": [
        "ps_get_bg_table"
      ]
    },
    {
      "page": "ps_hit_score_plot",
      "title": "Hit Position Against Hit Score",
      "topics": [
        "ps_hit_score_plot"
      ]
    },
    {
      "page": "ps_hitpos_map",
      "title": "Heatmap of Motif Hit Positions from Pscan Results",
      "topics": [
        "ps_hitpos_map"
      ]
    },
    {
      "page": "ps_hits_oligo",
      "title": "Retrieve Matched Oligonucleotide Sequences (Generic Function)",
      "topics": [
        "ps_hits_oligo"
      ]
    },
    {
      "page": "ps_hits_oligo_bg",
      "title": "Retrieve Matched Oligonucleotide Sequences from a Background Dataset (Generic Function)",
      "topics": [
        "ps_hits_oligo_bg"
      ]
    },
    {
      "page": "ps_hits_oligo_bg-PSMatrix-method",
      "title": "Get Matched Oligonucleotide Sequences of a Background Dataset",
      "topics": [
        "ps_hits_oligo_bg,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_oligo-PSMatrix-method",
      "title": "Get Matched Oligonucleotide Sequences",
      "topics": [
        "ps_hits_oligo,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_pos",
      "title": "Retrieve Motif Hit Positions (Generic Function)",
      "topics": [
        "ps_hits_pos"
      ]
    },
    {
      "page": "ps_hits_pos_bg",
      "title": "Retrieve Motif Hit Positions on Background Dataset (Generic Function)",
      "topics": [
        "ps_hits_pos_bg"
      ]
    },
    {
      "page": "ps_hits_pos_bg-PSMatrix-method",
      "title": "Get Motif Hit Positions in a Background Dataset",
      "topics": [
        "ps_hits_pos_bg,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_pos-PSMatrix-method",
      "title": "Get Motif Hit Positions",
      "topics": [
        "ps_hits_pos,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_score",
      "title": "Retrieve Motif Hit Scores (Generic Function)",
      "topics": [
        "ps_hits_score"
      ]
    },
    {
      "page": "ps_hits_score_bg",
      "title": "Retrieve Motif Hit Scores from a Background Dataset (Generic Function)",
      "topics": [
        "ps_hits_score_bg"
      ]
    },
    {
      "page": "ps_hits_score_bg-PSMatrix-method",
      "title": "Get Hits Score for Background Dataset",
      "topics": [
        "ps_hits_score_bg,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_score-PSMatrix-method",
      "title": "Get Hits Score",
      "topics": [
        "ps_hits_score,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_size",
      "title": "Retrieve the Hits Size Value for Motif Enrichment Analysis (Generic Function)",
      "topics": [
        "ps_hits_size"
      ]
    },
    {
      "page": "ps_hits_size-PSMatrix-method",
      "title": "Compute Hits Size",
      "topics": [
        "ps_hits_size,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_strand",
      "title": "Retrieve Motif Hit Strand Information (Generic Function)",
      "topics": [
        "ps_hits_strand"
      ]
    },
    {
      "page": "ps_hits_strand_bg",
      "title": "Retrieve Motif Hit Strand Information for the Background Dataset (Generic Function)",
      "topics": [
        "ps_hits_strand_bg"
      ]
    },
    {
      "page": "ps_hits_strand_bg-PSMatrix-method",
      "title": "Get Motif Hit Strand Information of a Background Dataset",
      "topics": [
        "ps_hits_strand_bg,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_strand-PSMatrix-method",
      "title": "Get Motif Hit Strand Information",
      "topics": [
        "ps_hits_strand,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_table",
      "title": "Retrieve a Summary Table of Motif Hits (Generic Function)",
      "topics": [
        "ps_hits_table"
      ]
    },
    {
      "page": "ps_hits_table-PSMatrix-method",
      "title": "Get Table of Motif Hits",
      "topics": [
        "ps_hits_table,PSMatrix-method"
      ]
    },
    {
      "page": "ps_hits_z",
      "title": "Compute Motif Hit Z-Scores (Generic Function)",
      "topics": [
        "ps_hits_z"
      ]
    },
    {
      "page": "ps_hits_z-PSMatrix-method",
      "title": "Get Motif Hit Z-score",
      "topics": [
        "ps_hits_z,PSMatrix-method"
      ]
    },
    {
      "page": "ps_load_select_transcripts",
      "title": "Load MANE Select and RefSeq Select Transcript Metadata",
      "topics": [
        "ps_load_select_transcripts"
      ]
    },
    {
      "page": "ps_motif_barplot",
      "title": "Bar Plot of the Most Enriched Motifs",
      "topics": [
        "ps_motif_barplot"
      ]
    },
    {
      "page": "ps_motif_class",
      "title": "Structural Class of Each Motif",
      "topics": [
        "ps_motif_class"
      ]
    },
    {
      "page": "ps_pvalue",
      "title": "Retrieve the Motif-Enrichment P-Value (Generic Function)",
      "topics": [
        "ps_pvalue"
      ]
    },
    {
      "page": "ps_pvalue-PSMatrix-method",
      "title": "Get P-Value",
      "topics": [
        "ps_pvalue,PSMatrix-method"
      ]
    },
    {
      "page": "ps_results_table",
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