sesame

DOI: 10.18129/B9.bioc.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 (3.14)

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

Installation

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

if (!requireNamespace("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")

 

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 1.11.10
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, graphics, KernSmooth, parallel, matrixStats, DNAcopy, stats, SummarizedExperiment, e1071
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_1.11.10.tar.gz
Windows Binary sesame_1.11.7.zip (32- & 64-bit)
macOS 10.13 (High Sierra) sesame_1.11.10.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

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