sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Bioconductor version: 3.23 · Package version: 1.30.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sesame")Details
| Maintainer | Wanding Zhou <zhouwanding@gmail.com> |
| Author | Wanding Zhou [aut, cre, fnd] (ORCID: <https://orcid.org/0000-0001-9126-1932>), Wubin Ding [ctb], David Goldberg [ctb], Ethan Moyer [ctb], Bret Barnes [ctb], Timothy Triche [ctb], Hui Shen [aut, fnd] |
| License | MIT + file LICENSE |
| URL | https://github.com/zwdzwd/sesame |
| Bug Reports | https://github.com/zwdzwd/sesame/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software |
| Package Short Url | https://bioconductor.org/packages/sesame/ |
Citation
From within R, enter citation("sesame"):
Wanding Zhou, Hui Shen. sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips. doi:10.18129/B9.bioc.sesame, R package version 1.30.1, https://bioconductor.org/packages/sesame.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Basic Usage & Preprocessing
- Sample Metadata Inference
- Quality Control
- Working with Non-human Array
- Modeling
Download
Follow the installation instructions to use this package in your R session.
| Source package | sesame_1.30.1.tar.gz |
| Windows binary (x86_64) | sesame_1.30.1.zip |
| macOS binary (arm64) | sesame_1.30.1.tgz |
| macOS binary (x86_64) | sesame_1.30.1.tgz |
Dependencies
Depends: R (>= 4.5.0), sesameData
Imports: graphics, BiocParallel, utils, methods, stringr, readr, tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1), IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, Seqinfo, stats, SummarizedExperiment (>= 1.39.1), dplyr, reshape2
Suggests: scales, BiocManager, GenomeInfoDb, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals
Reverse dependencies
Imports Me (3): CytoMethIC, MethReg, TENET
Suggests Me (4): knowYourCG, RnBeads, sesameData, TCGAbiolinks