generegulation
Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching
Bioconductor version: Release (3.17)
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("generegulation")):
Installation
To install this package, start R (version "4.3") 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")| Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching | HTML | R Script |
Details
| biocViews | EpigeneticsWorkflow, Workflow |
| Version | 1.24.0 |
| 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 | |
| Linking To | |
| Suggests | knitr, rmarkdown, BiocStyle |
| System Requirements | |
| Enhances | |
| URL | https://www.bioconductor.org/help/workflows/generegulation/ |
See More
| 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_1.24.0.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 |