sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Bioconductor version: 3.23 · Package version: 1.30.1
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 |
| Downloads rank | 1380 |
| Source branch | RELEASE_3_23 |
| biocViews | DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software |
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