FlowSorted.Blood.EPIC

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

Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells

Bioconductor version: Release (3.15)

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	2.0.0
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_2.0.0.tar.gz
Windows Binary
macOS Binary (x86_64)
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