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sesame

This is the development version of sesame; for the stable release version, see sesame.

SEnsible Step-wise Analysis of DNA MEthylation BeadChips


Bioconductor version: Development (3.19)

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.

Author: Wanding Zhou [aut, cre] , Wubin Ding [ctb], David Goldberg [ctb], Ethan Moyer [ctb], Bret Barnes [ctb], Timothy Triche [ctb], Hui Shen [aut]

Maintainer: Wanding Zhou <zhouwanding at gmail.com>

Citation (from within R, enter citation("sesame")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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. knowYourCG HTML R Script
Reference Manual PDF

Details

biocViews DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software
Version 1.21.15
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License MIT + file LICENSE
Depends R (>= 4.3.0), sesameData
Imports graphics, BiocParallel, utils, methods, stringr, readr, tibble, illuminaio, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2
System Requirements
URL https://github.com/zwdzwd/sesame
Bug Reports https://github.com/zwdzwd/sesame/issues
See More
Suggests scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals
Linking To
Enhances
Depends On Me
Imports Me CytoMethIC, MethReg
Suggests Me knowYourCG, 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_1.21.15.tar.gz
Windows Binary
macOS Binary (x86_64) sesame_1.21.15.tgz
macOS Binary (arm64)
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