generegulation

DOI: 10.18129/B9.bioc.generegulation  

Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching

Bioconductor version: Release (3.16)

The binding of transcription factor proteins (TFs) to DNA promoter regions upstream of gene transcription start sites (TSSs) is one of the most important mechanisms by which gene expression, and thus many cellular processes, are controlled. Though in recent years many new kinds of data have become available for identifying transcription factor binding sites (TFBSs) -- ChIP-seq and DNase I hypersensitivity regions among them -- sequence matching continues to play an important role. In this workflow we demonstrate Bioconductor techniques for finding candidate TF binding sites in DNA sequence using the model organism Saccharomyces cerevisiae. The methods demonstrated here apply equally well to other organisms.

Author: Bioconductor Package Maintainer [aut, cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("generegulation")

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("generegulation")

 

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R Script

Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching

Details

biocViews	EpigeneticsWorkflow, Workflow
Version	1.22.0
License	Artistic-2.0
Depends	R (>= 3.3.0), BSgenome.Scerevisiae.UCSC.sacCer3, Biostrings, GenomicFeatures, MotifDb, S4Vectors, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, motifStack, org.Sc.sgd.db, seqLogo
Imports
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://www.bioconductor.org/help/workflows/generegulation/
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	generegulation_1.22.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/generegulation
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/generegulation
Package Short Url	https://bioconductor.org/packages/generegulation/
Package Downloads Report	Download Stats