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 (from within R, enter 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 PDF
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