FlowSorted.Blood.EPIC

DOI: 10.18129/B9.bioc.FlowSorted.Blood.EPIC  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see FlowSorted.Blood.EPIC.

Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells

Bioconductor version: 3.16

Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.

Author: Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi)

Maintainer: Lucas A. Salas <lucas.a.salas.diaz at dartmouth.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FlowSorted.Blood.EPIC")

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("FlowSorted.Blood.EPIC")

 

HTML	R Script	FlowSorted.Blood.EPIC
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, Tissue, TissueMicroarrayData
Version	2.2.0
License	GPL-3
Depends	R (>= 3.5), minfi(>= 1.21.2), ExperimentHub
Imports	genefilter, nlme, quadprog, graphics, stats, utils, AnnotationHub, SummarizedExperiment, S4Vectors
LinkingTo
Suggests	knitr, rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19
SystemRequirements
Enhances	FlowSorted.CordBloodCombined.450k(>= 1.11.5)
URL	https://github.com/immunomethylomics/FlowSorted.Blood.EPIC
BugReports	https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues.
Depends On Me
Imports Me
Suggests Me	DMRcate, FlowSorted.CordBloodCombined.450k, wateRmelon
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	FlowSorted.Blood.EPIC_2.2.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FlowSorted.Blood.EPIC
Package Short Url	https://bioconductor.org/packages/FlowSorted.Blood.EPIC/
Package Downloads Report	Download Stats