FlowSorted.Blood.EPIC
Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
Bioconductor version: Release (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("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 | 2.10.0 |
| 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_2.10.0.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 |