Introduction | How to estimate cell-type fractions in blood | How to estimate generic cell-type fractions in a solid tissue | How to estimate immune cell-type fractions in a solid tissue using HEpiDISH | More info about different methods for cell-type fractions estimation | How to identify differentially methylated cell-types in EWAS | Sessioninfo | References
Package: EpiDISH 2.29.0
Shijie C. Zheng
EpiDISH: Epigenetic Dissection of Intra-Sample-Heterogeneity
EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of blood-tissue of any age, from birth to old-age, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.
Authors:
EpiDISH_2.29.0.tar.gz
EpiDISH_2.29.0.zip(r-4.7)EpiDISH_2.29.0.zip(r-4.6)EpiDISH_2.29.0.zip(r-4.5)
EpiDISH_2.29.0.tgz(r-4.6-any)EpiDISH_2.29.0.tgz(r-4.5-any)
EpiDISH_2.29.0.tar.gz(r-4.7-any)EpiDISH_2.29.0.tar.gz(r-4.6-any)
EpiDISH_2.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EpiDISH/json (API)
| # Install 'EpiDISH' in R: |
| install.packages('EpiDISH', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sjczheng/epidish/issues
Datasets:
- cent12CT.m - Whole blood reference of 12 blood cell subtypes for EPIC array
- cent12CT450k.m - Whole blood reference of 12 blood cell subtypes for 450k array
- centBloodSub.m - Whole blood reference of 188 tsDHS-DMCs and 7 blood cell subtypes
- centDHSbloodDMC.m - Whole blood reference of 333 tsDHS-DMCs and 7 blood cell subtypes
- centEpiFibFatIC.m - Reference for breast tissue
- centEpiFibIC.m - Reference for genenric epithelial tissue
- centUniLIFE.m - DNAm reference matrix for 19 immune cell-types for blood of any age
- DummyBeta.m - Dummy beta value matrix
- LiuDataSub.m - Whole blood example beta value matrix
On BioConductor:EpiDISH-2.29.0(bioc 3.24)EpiDISH-2.28.0(bioc 3.23)
dnamethylationmethylationarrayepigeneticsdifferentialmethylationimmunooncology
Last updated from:589b601243. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 183 | ||
| linux-devel-x86_64 | NOTE | 254 | ||
| source / vignettes | OK | 217 | ||
| linux-release-x86_64 | NOTE | 251 | ||
| macos-release-arm64 | NOTE | 133 | ||
| macos-oldrel-arm64 | NOTE | 136 | ||
| windows-devel | NOTE | 174 | ||
| windows-release | NOTE | 151 | ||
| windows-oldrel | NOTE | 154 | ||
| wasm-release | OK | 136 |
Exports:CellDMCConstructDNAmPanelDoMetaEfronepidishhepidish
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclassclicpp11crayoncurlDBIe1071fastmapgenefiltergenericsgluehttrIRangesjsonliteKEGGRESTlatticelifecyclelocfdrmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngproxyquadprogR6rlangRSQLiteS4VectorsSeqinfostringistringrsurvivalsysvctrsXMLxtableXVector
