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 (3.24)
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]
Maintainer: Peyman Zarrineh <peyman.zarrineh at manchester.ac.uk>
citation("Motif2Site")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("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 | 1.17.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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/fls-bioinformatics-core/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_1.17.0.tar.gz |
| Windows Binary (x86_64) | Motif2Site_1.17.0.zip |
| macOS Binary (big-sur-x86_64) | Motif2Site_1.17.0.tgz |
| macOS Binary (sonoma-arm64) | Motif2Site_1.17.0.tgz |
| 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 |