sesame
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see sesame.
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Bioconductor version: 3.14
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 more accurate detection calling, intelligenet inference of ethnicity, sex and advanced quality control routines.
Author: Wanding Zhou [aut, cre], Hui Shen [aut], Timothy Triche [ctb], Bret Barnes [ctb]
Maintainer: Wanding Zhou <zhouwanding at gmail.com>
citation("sesame")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sesame")
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("sesame")| 0. Basic Usage | HTML | R Script |
| 1. Quality Control | HTML | R Script |
| 2. Non-human Array | HTML | R Script |
| 3. Modeling | HTML | R Script |
| 4. Data Inference | HTML | R Script |
| 5. Other Features | HTML | R Script |
| 6. knowYourCG | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software |
| Version | 1.12.9 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1), sesameData, methods |
| Imports | BiocParallel, grDevices, utils, stringr, tibble, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, randomForest, wheatmap, ggplot2, graphics, KernSmooth, parallel, matrixStats, DNAcopy, stats, SummarizedExperiment, e1071, fgsea, ggrepel, reshape2 |
| System Requirements | |
| URL | https://github.com/zwdzwd/sesame |
| Bug Reports | https://github.com/zwdzwd/sesame/issues |
See More
| Suggests | scales, knitr, rmarkdown, testthat, dplyr, tidyr, BiocStyle, IlluminaHumanMethylation450kmanifest, minfi, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, HDF5Array |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | TCGAbiolinksGUI |
| Suggests Me | MethReg, RnBeads, sesameData, TCGAbiolinks |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sesame_1.12.9.tar.gz |
| Windows Binary | sesame_1.12.9.zip |
| macOS 10.13 (High Sierra) | sesame_1.12.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sesame |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sesame |
| Bioc Package Browser | https://code.bioconductor.org/browse/sesame/ |
| Package Short Url | https://bioconductor.org/packages/sesame/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |