PscanR
This is the development version of PscanR; to use it, please install the devel version of Bioconductor.
Motif Enrichment Analysis of Regulatory DNA Sequences
Bioconductor version: Development (3.24)
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.
Author: Federico Zambelli [aut, cre] 
, Giulio Pavesi [aut] , Diana Betelli [ctb], Italy's National Recovery and Resilience Plan (PNRR) [fnd] (project ELIXIRNextGenIT, R0000010)
Maintainer: Federico Zambelli <federico.zambelli at unimi.it>
citation("PscanR")):Federico Zambelli, Giulio Pavesi. PscanR: Motif Enrichment Analysis of Regulatory DNA Sequences. doi:10.18129/B9.bioc.PscanR, R package version 0.99.3, https://bioconductor.org/packages/PscanR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("PscanR")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("PscanR")| Building a background for PscanR | HTML |
| Motif enrichment analysis with PscanR: Arabidopsis BPC target promoters | HTML |
| Motif enrichment analysis with PscanR: mouse retinal promoters | HTML |
| PscanR Concepts and Input Preparation | HTML |
| PscanR Quick Overview | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | GeneRegulation, MotifAnnotation, SequenceMatching, Software, Transcription |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | BiocFileCache, BiocParallel, BiocGenerics, Biostrings, ExperimentHub, ggplot2, grDevices, methods, pheatmap, RSQLite, stats, TFBSTools, UCSC.utils, utils |
| System Requirements | |
| URL | https://github.com/Federico77z/PscanR |
| Bug Reports | https://github.com/Federico77z/PscanR/issues |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/PscanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PscanR |
| Package Short Url | https://bioconductor.org/packages/PscanR/ |
| Package Downloads Report | Download Stats |