Workflow Package: generegulation

Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("generegulation")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("generegulation", version = "3.8")

Documentation

To view available workflows for the version of this package installed in your system, start R and enter:

browseVignettes("generegulation")

 

HTML R Script Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching

Details

biocViews EpigeneticsWorkflow, Workflow
Version 1.4.0
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
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