This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see sesame.
Bioconductor version: 3.12
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")
):
To install this package, start R (version "4.0") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sesame")
HTML | R Script | 0. SeSAMe User Guide |
HTML | R Script | 1. Quality Controls |
HTML | R Script | 2. Large Data |
HTML | R Script | 3. Minfi Interaction |
HTML | R Script | 4. data sanitization |
HTML | R Script | 5. Horvath Mammal40 Array |
HTML | R Script | 6. Mouse Array |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | DNAMethylation, MethylationArray, Preprocessing, QualityControl, Software |
Version | 1.8.12 |
In Bioconductor since | BioC 3.8 (R-3.5) (2.5 years) |
License | MIT + file LICENSE |
Depends | R (>= 4.0), sesameData, methods |
Imports | BiocParallel, grDevices, utils, stringr, tibble, illuminaio, MASS, GenomicRanges, IRanges, grid, preprocessCore, S4Vectors, randomForest, wheatmap, ggplot2, 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 | sesameData, TCGAbiolinks |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | sesame_1.8.12.tar.gz |
Windows Binary | sesame_1.8.10.zip |
macOS 10.13 (High Sierra) | sesame_1.8.12.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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