sesame

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see sesame.

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Bioconductor version: 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 iD ORCID: 0000-0001-9126-1932 , 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")
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 1.26.0

In Bioconductor since BioC 3.8 (R-3.5) (7 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, TENET, 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_1.26.0.tar.gz

Windows Binary (x86_64) sesame_1.26.0.zip

macOS Binary (x86_64) sesame_1.26.0.tgz

macOS Binary (arm64) sesame_1.26.0.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