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recountmethylation
This is thedevelopment version of recountmethylation; for the stable release version, seerecountmethylation.
Access and analyze public DNA methylation array data compilations
Bioconductor version: Development (3.23)
Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.
Author: Sean K Maden [cre, aut]
ORCID: 0000-0002-2212-4894, Brian Walsh [aut] ORCID: 0000-0003-0913-1528, Kyle Ellrott [aut] ORCID: 0000-0002-6573-5900, Kasper D Hansen [aut] ORCID: 0000-0003-0086-0687, Reid F Thompson [aut] ORCID: 0000-0003-3661-5296, Abhinav Nellore [aut] ORCID: 0000-0001-8145-1484
Maintainer: Sean K Maden <maden at ohsu.edu>
citation("recountmethylation")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("recountmethylation")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("recountmethylation")| Data Analyses | HTML | R Script |
| Determine population ancestry from DNAm arrays | HTML | R Script |
| Nearest neighbors analysis for DNAm arrays | HTML | R Script |
| Power analysis for DNAm arrays | HTML | R Script |
| Practical uses for CpG annotations | HTML | R Script |
| recountmethylation User's Guide | HTML | R Script |
| Working with DNAm data types | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation,Epigenetics,ExperimentHub,MethylationArray,Microarray,Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1) |
| Imports | minfi,HDF5Array,rhdf5,S4Vectors, utils, methods,RCurl,R.utils,BiocFileCache,basilisk,reticulate,DelayedMatrixStats |
| System Requirements | |
| URL | https://github.com/metamaden/recountmethylation |
| Bug Reports | https://github.com/metamaden/recountmethylation/issues |
See More
| Suggests | minfiData,minfiDataEPIC,knitr,testthat,ggplot2,gridExtra,rmarkdown,BiocStyle,GenomicRanges,limma,ExperimentHub,AnnotationHub |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | recountmethylation_1.21.0.tar.gz |
| Windows Binary (x86_64) | recountmethylation_1.21.0.zip |
| macOS Binary (x86_64) | recountmethylation_1.21.0.tgz |
| macOS Binary (arm64) | recountmethylation_1.21.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/recountmethylation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/recountmethylation |
| Bioc Package Browser | https://code.bioconductor.org/browse/recountmethylation/ |
| Package Short Url | https://bioconductor.org/packages/recountmethylation/ |
| Package Downloads Report | Download Stats |