Advanced user deconvolution CP/QP, CIBERSORT and/or RPC deconvolution
Package: FlowSorted.Blood.EPIC 2.16.0
Lucas A. Salas
FlowSorted.Blood.EPIC: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
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.
Authors:
FlowSorted.Blood.EPIC_2.16.0.tar.gz
FlowSorted.Blood.EPIC_2.16.0.tar.gz(r-4.7-any)FlowSorted.Blood.EPIC_2.16.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FlowSorted.Blood.EPIC/json (API)
| # Install 'FlowSorted.Blood.EPIC' in R: |
| install.packages('FlowSorted.Blood.EPIC', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/immunomethylomics/flowsorted.blood.epic/issues
Datasets:
- IDOLOptimizedCpGs - IDOL Optimized CpGs for adult blood DNA methylation deconvolution EPIC
- IDOLOptimizedCpGs.compTable - IDOL Optimized CpGs matrix for adult blood DNA methylation deconvolution EPIC
- IDOLOptimizedCpGs450klegacy - IDOL Optimized CpGs for adult blood DNA methylation deconvolution EPIC
- IDOLOptimizedCpGs450klegacy.compTable - IDOL Optimized CpGs matrix for adult blood DNA methylation deconvolution EPIC
- IDOLOptimizedCpGsCordBlood - IDOL Optimized CpGs for umbilical cord blood DNA methylation deconvolution
On BioConductor:FlowSorted.Blood.EPIC-2.17.2(data/experiment 3.24)FlowSorted.Blood.EPIC-2.16.0(data/experiment 3.23)
experimentdatahomo_sapiens_datatissuemicroarraydatagenometissuemicroarraydatamethylationarraydatadatapkg
Last updated from:a88844dcb3 (on RELEASE_3_23). Checks:1 WARNING, 2 NOTE, 1 OK. Indexed: no.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 363 | ||
| linux-devel | NOTE | 901 | ||
| source / vignettes | OK | 726 | ||
| linux-release | NOTE | 1009 |
Exports:estimateCellCounts2libraryDataGetprojectCellType_CP
Dependencies:abindannotateAnnotationDbiAnnotationHubaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbumphuntercachemcigarilloclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrExperimentHubfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueh5mreadHDF5Arrayhmshttrhttr2illuminaioIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscrimeselectrSeqinfosiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbutf8vctrsvroomwithrXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| estimateCellCounts2 | estimateCellCounts2 |
| FlowSorted.Blood.EPIC | FlowSorted.Blood.EPIC |
| IDOL Optimized CpGs for adult blood DNA methylation deconvolution EPIC | IDOLOptimizedCpGs |
| IDOL Optimized CpGs matrix for adult blood DNA methylation deconvolution EPIC | IDOLOptimizedCpGs.compTable |
| IDOL Optimized CpGs for adult blood DNA methylation deconvolution EPIC | IDOLOptimizedCpGs450klegacy |
| IDOL Optimized CpGs matrix for adult blood DNA methylation deconvolution EPIC | IDOLOptimizedCpGs450klegacy.compTable |
| IDOL Optimized CpGs for umbilical cord blood DNA methylation deconvolution | IDOLOptimizedCpGsCordBlood |
| libraryDataGet | libraryDataGet |
| projectCellType_CP | projectCellType_CP |