sesame

DOI: 10.18129/B9.bioc.sesame    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see sesame.

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software
Version	1.10.5
In Bioconductor since	BioC 3.8 (R-3.5) (3 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, KernSmooth, graphics, parallel, matrixStats, DNAcopy, stats, SummarizedExperiment
LinkingTo
Suggests	scales, knitr, rmarkdown, testthat, dplyr, tidyr, BiocStyle, IlluminaHumanMethylation450kmanifest, minfi, FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k, HDF5Array
SystemRequirements
Enhances
URL	https://github.com/zwdzwd/sesame
BugReports	https://github.com/zwdzwd/sesame/issues
Depends On Me
Imports Me	TCGAbiolinksGUI
Suggests Me	MethReg, RnBeads, sesameData, TCGAbiolinks
Links To Me
Build Report

Package Archives

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

Source Package	sesame_1.10.5.tar.gz
Windows Binary	sesame_1.10.5.zip
macOS 10.13 (High Sierra)	sesame_1.10.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sesame
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sesame
Package Short Url	https://bioconductor.org/packages/sesame/
Package Downloads Report	Download Stats