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 (3.21)

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] (ORCID: ), 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 "4.5") 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
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software
Version	1.25.2
In Bioconductor since	BioC 3.8 (R-3.5) (6 years)
License	MIT + file LICENSE
Depends	R (>= 4.5.0), sesameData
Imports	graphics, BiocParallel, utils, methods, stringr, readr, tibble, 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

Suggests	scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals
Linking To
Enhances
Depends On Me
Imports Me	MethReg, CytoMethIC
Suggests Me	knowYourCG, RnBeads, TCGAbiolinks, sesameData
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	sesame_1.25.2.tar.gz
Windows Binary (x86_64)	sesame_1.25.2.zip
macOS Binary (x86_64)	sesame_1.25.2.tgz
macOS Binary (arm64)	sesame_1.25.2.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