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FlowSorted.Blood.EPIC

This is the development version of FlowSorted.Blood.EPIC; for the stable release version, see FlowSorted.Blood.EPIC.

Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells


Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("FlowSorted.Blood.EPIC")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews ExperimentData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, Tissue, TissueMicroarrayData
Version 2.9.0
License GPL-3
Depends R (>= 3.5), minfi(>= 1.21.2), ExperimentHub
Imports genefilter, nlme, quadprog, graphics, stats, utils, AnnotationHub, SummarizedExperiment, S4Vectors
System Requirements
URL https://github.com/immunomethylomics/FlowSorted.Blood.EPIC
Bug Reports https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues.
See More
Suggests knitr, rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Linking To
Enhances FlowSorted.CordBloodCombined.450k(>= 1.11.5)
Depends On Me
Imports Me HiBED
Suggests Me DMRcate, wateRmelon, FlowSorted.CordBloodCombined.450k
Links To Me
Build Report Build Report

Package Archives

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

Source Package FlowSorted.Blood.EPIC_2.9.0.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/
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