Package: PscanR 0.99.0

Federico Zambelli

PscanR: Motif Enrichment Analysis of Regulatory DNA Sequences

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.

Authors:Federico Zambelli [aut, cre], Giulio Pavesi [aut], Diana Betelli [ctb]

PscanR_0.99.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PscanR/json (API)

# Install 'PscanR' in R:
install.packages('PscanR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/federico77z/pscanr/issues

On CRAN:

Conda:

sequencematchingtranscriptiongeneregulationmotifannotation

4.30 score 7 scripts 49 exports 98 dependencies

Last updated from:3d1af59dab. Checks:1 NOTE, 9 OK. Indexed: yes.
A new build is currently in progress.

TargetResultTimeFilesSyslog
bioc-checksNOTE384
linux-develOK535
source / vignettesOK509
linux-releaseOK529
macos-releaseOK406
macos-oldrelOK356
windows-develOK451
windows-releaseOK416
windows-oldrelOK410
wasm-releaseOK262

Exports:ps_available_bgps_bg_avgps_bg_avg<-ps_bg_seq_namesps_bg_sizeps_bg_size<-ps_bg_std_devps_bg_std_dev<-ps_build_bgps_build_bg_from_tableps_density_plotps_fg_avgps_fg_sizeps_get_bg_tableps_hit_score_plotps_hitpos_mapps_hits_oligops_hits_oligo_bgps_hits_posps_hits_pos_bgps_hits_scoreps_hits_score_bgps_hits_sizeps_hits_strandps_hits_strand_bgps_hits_tableps_hits_zps_load_select_transcriptsps_motif_barplotps_motif_classps_pvalueps_results_tableps_retrieve_bgps_retrieve_bg_from_fileps_scanps_select_promotersps_selection_summaryps_seq_namesps_transcript_legendps_write_bg_to_fileps_z_tableps_zscoreps_zscore_heatmappscanpscan_filteredpscan_full_bgPSMatrixPSMatrixListshow

Dependencies:AnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomecachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIdbplyrDirichletMultinomialdplyrExperimentHubfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlifecyclemagrittrmatrixStatsmemoisemimeopensslpheatmappillarpkgconfigpngpurrrpwalignR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4VectorsS7scalesSeqinfoseqLogosnowstringistringrsysTFBSToolsTFMPvaluetibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

PscanR Concepts and Input Preparation
Installation | Introduction | Relationship to other motif tools | Workflow overview | The background model | Obtaining a precomputed background | Preparing promoter sequences for pscan() | Scanning from a list of transcripts | Selecting promoters from a gene list | Configuring parallel execution | Data provenance | Session information
Rendered fromPscanR_concepts_and_input.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-09-09

Motif enrichment analysis with PscanR: mouse retinal promoters
Installation | Introduction | The data | The background | From genes to promoters | A small executable scan | Running the scan | Checking the result against a second gene set | Comparison with the published figure | Inspecting the result object | Motif score patterns across promoters | Positional distribution of motif matches | Analysing a motif-selected promoter subset | Summary | Appendix: Comparison with the published analysis | Data provenance | Session information
Rendered fromPscanR_Mouse_HD_Retina.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-09-09

Motif enrichment analysis with PscanR: Arabidopsis BPC target promoters
Installation | Introduction | The data | The background | From genes to promoters | A small executable scan | Running the scan | Inspecting the result object | Motif score patterns across promoters | Positional distribution of motif matches | Analysing a motif-selected promoter subset | Summary | Appendix: Comparison with the published analysis | Data provenance | Session information
Rendered fromPscanR_Arabidopsis_BPC.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-09-09

PscanR Quick Overview
Introduction | Installation | An executable workflow | Table 1: Motif enrichment analysis and input preparation | Table 2: Background construction | Table 3: Result summaries and visualisation | Data provenance | Session information
Rendered fromPscanRQuickOverview.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2025-05-27

Building a background for PscanR
Installation | Introduction | A small executable construction and round trip | Part A: Building a standard background | The promoters | The matrices | Building a standard background | Saving and reloading a standard background | Verification against the catalogue | Part B: Building and querying a full background | Saving and reloading a full background | Analysing a foreground by identifier | Part C: Checklist for a new background | Summary | Data provenance | Session information
Rendered fromPscanR_Custom_Background.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-09-09

Readme and manuals

Help Manual

Help pageTopics
Get Available Pre-Computed Background Filesps_available_bg
Retrieve the Background Average Score for Motif Enrichment Analysis (Generic Function)ps_bg_avg
Get Background Average Scoreps_bg_avg,PSMatrix-method
Generic Setter Method for Background Mean Value of an objectps_bg_avg<-
Set Background Averageps_bg_avg<-,PSMatrix-method
Retrieve Sequence Names for the Background Dataset (Generic Function)ps_bg_seq_names
Get Sequence Identifiers of the Background Datasetps_bg_seq_names,PSMatrix-method
Retrieve the Background Size Value for Motif Enrichment Analysis (Generic Function)ps_bg_size
Get Background Sizeps_bg_size,PSMatrix-method
Set Background Size (Generic Function)ps_bg_size<-
Set Background Size in a PSMatrixps_bg_size<-,PSMatrix-method
Retrieve the Background Standard Deviation for Motif Enrichment Analysis (Generic Function)ps_bg_std_dev
Get Background Standard Deviationps_bg_std_dev,PSMatrix-method
Set Background Standard Deviation (Generic Function)ps_bg_std_dev<-
Set Background Standard Deviationps_bg_std_dev<-,PSMatrix-method
Build background matrices in parallelps_build_bg
Apply background parameters to position frequency matricesps_build_bg_from_table
Density Plot of Motif Hits Along Promoter Regionsps_density_plot
Retrieve the Foreground Average Score for Motif Enrichment Analysis (Generic Function)ps_fg_avg
Get Foreground Average Scoreps_fg_avg,PSMatrix-method
Retrieve the Foreground Size Value for Motif Enrichment Analysis (Generic Function)ps_fg_size
Get Foreground Sizeps_fg_size,PSMatrix-method
Extract background statistics from a `PSMatrixList` objectps_get_bg_table
Hit Position Against Hit Scoreps_hit_score_plot
Heatmap of Motif Hit Positions from Pscan Resultsps_hitpos_map
Retrieve Matched Oligonucleotide Sequences (Generic Function)ps_hits_oligo
Retrieve Matched Oligonucleotide Sequences from a Background Dataset (Generic Function)ps_hits_oligo_bg
Get Matched Oligonucleotide Sequences of a Background Datasetps_hits_oligo_bg,PSMatrix-method
Get Matched Oligonucleotide Sequencesps_hits_oligo,PSMatrix-method
Retrieve Motif Hit Positions (Generic Function)ps_hits_pos
Retrieve Motif Hit Positions on Background Dataset (Generic Function)ps_hits_pos_bg
Get Motif Hit Positions in a Background Datasetps_hits_pos_bg,PSMatrix-method
Get Motif Hit Positionsps_hits_pos,PSMatrix-method
Retrieve Motif Hit Scores (Generic Function)ps_hits_score
Retrieve Motif Hit Scores from a Background Dataset (Generic Function)ps_hits_score_bg
Get Hits Score for Background Datasetps_hits_score_bg,PSMatrix-method
Get Hits Scoreps_hits_score,PSMatrix-method
Retrieve the Hits Size Value for Motif Enrichment Analysis (Generic Function)ps_hits_size
Compute Hits Sizeps_hits_size,PSMatrix-method
Retrieve Motif Hit Strand Information (Generic Function)ps_hits_strand
Retrieve Motif Hit Strand Information for the Background Dataset (Generic Function)ps_hits_strand_bg
Get Motif Hit Strand Information of a Background Datasetps_hits_strand_bg,PSMatrix-method
Get Motif Hit Strand Informationps_hits_strand,PSMatrix-method
Retrieve a Summary Table of Motif Hits (Generic Function)ps_hits_table
Get Table of Motif Hitsps_hits_table,PSMatrix-method
Compute Motif Hit Z-Scores (Generic Function)ps_hits_z
Get Motif Hit Z-scoreps_hits_z,PSMatrix-method
Load MANE Select and RefSeq Select Transcript Metadataps_load_select_transcripts
Bar Plot of the Most Enriched Motifsps_motif_barplot
Structural Class of Each Motifps_motif_class
Retrieve the Motif-Enrichment P-Value (Generic Function)ps_pvalue
Get P-Valueps_pvalue,PSMatrix-method
Create a Summary Table of PscanR Resultsps_results_table
Generate PSMatrixList from Background data and JASPAR Matrixps_retrieve_bg
Import background-scored matrices from a fileps_retrieve_bg_from_file
Perform Motif Scanning (Generic Function)ps_scan
Perform a Scan of DNA Sequences Using a `PSMatrix` Objectps_scan,PSMatrix-method
Select One Representative Promoter per Geneps_select_promoters
Summarise a Promoter Selectionps_selection_summary
Retrieve Sequence Names (Generic Function)ps_seq_names
Get Sequence Namesps_seq_names,PSMatrix-method
Transcript ID Legend (Generic Function)ps_transcript_legend
Get the Transcript ID Legend from a PSMatrixList objectps_transcript_legend,PSMatrixList-method
Save background statistics from a `PSMatrixList` object to a fileps_write_bg_to_file
Generate a Z-score Matrix of Motif Enrichment per Sequenceps_z_table
Retrieve the Motif-Enrichment Z-Score (Generic Function)ps_zscore
Heatmap of Per-Sequence Motif Z-Scoresps_zscore_heatmap
Get Z-Scoreps_zscore,PSMatrix-method
Executes the Pscan algorithm on a set of regulatory sequences.pscan
Filter and Scan Promoter Regions with Pscanpscan_filtered
Extract Pre-Computed Metrics from a PSMatrixList Objectpscan_full_bg
An S4 Class for a Single Position-Specific MatrixPSMatrix setAs,PFMatrix,PSMatrix-method
An S4 Class for Storing Position-Specific MatricesPSMatrixList setAs,PFMatrixList,PSMatrixList-method
Display Details of a `PSMatrix` objectshow,PSMatrix-method