FlowSorted.Blood.EPIC
This package is for version 3.19 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: 3.19
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("FlowSorted.Blood.EPIC")):
Installation
To install this package, start R (version "4.4") 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")| FlowSorted.Blood.EPIC | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, Tissue, TissueMicroarrayData |
| Version | 2.8.0 |
| 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_2.8.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |