Motif2Site
This is the development version of Motif2Site; for the stable release version, see Motif2Site.
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
Bioconductor version: Development (3.21)
Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.
Author: Peyman Zarrineh [cre, aut] (ORCID:
Maintainer: Peyman Zarrineh <peyman.zarrineh at manchester.ac.uk>
citation("Motif2Site")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("Motif2Site")
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("Motif2Site")| Motif2Site | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, DifferentialPeakCalling, Epigenetics, SequenceMatching, Sequencing, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.1) |
| Imports | S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/ManchesterBioinference/Motif2Site/issues |
See More
| Suggests | BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Motif2Site_1.11.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/Motif2Site |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Motif2Site |
| Bioc Package Browser | https://code.bioconductor.org/browse/Motif2Site/ |
| Package Short Url | https://bioconductor.org/packages/Motif2Site/ |
| Package Downloads Report | Download Stats |