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Bioconductor - sesame

sesame

This is the released version of sesame; for the devel version, see sesame.

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Bioconductor version: Release (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: 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")
Details biocViews DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software Version 1.26.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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 See More 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.

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