Package: decemedip 1.1.0

Ning Shen

decemedip: hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methylome

The R package decemedip is a novel computational paradigm developed for inferring the relative abundances of cell types and tissues measure by methylated DNA immunoprecipitation sequencing (MeDIP-Seq). This paradigm allows using reference data from other technologies such as microarray or WGBS.

Authors:Ning Shen [aut, cre]

decemedip_1.1.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
decemedip/json (API)
NEWS

# Install 'decemedip' in R:
install.packages('decemedip', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nshen7/decemedip/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • example.hg19.ref.anc.se - Subset of hg19.ref.anc.se as a lightweighted example
  • example.hg19.ref.cts.se - Subset of hg19.ref.cts.se as a lightweighted example
  • example.pdx.counts.anc.se - Subset of pdx.counts.anc.se as a lightweighted example
  • example.pdx.counts.cts.se - Subset of pdx.counts.cts.se as a lightweighted example
  • hg19.ref.anc.se - Hg19 genomic information of anchor CpGs (i.e., all-tissue unmethylated/methylation probes) inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6). Used as default in 'decemedip'.
  • hg19.ref.cts.se - Hg19 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).
  • hg38.ref.anc.se - Hg38 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).
  • hg38.ref.cts.se - Hg38 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).
  • pdx.counts.anc.se - MeDIP-seq read counts on reference anchor CpGs of 3 PDX samples from Berchuck et al. 2022
  • pdx.counts.cts.se - MeDIP-seq read counts on reference cell type-specific CpGs of 3 PDX samples from Berchuck et al. 2022

On BioConductor:decemedip-1.1.0(bioc 3.24)decemedip-1.0.0(bioc 3.23)

softwareimmunooncologydnamethylationepigeneticssequencingwholegenomebayesianbayesian-data-analysisbayesian-inferencebioinformaticsdna-methylationdna-methylation-dataepigenomicsgenerative-modelomicsrstanstancpp

5.41 score 4 stars 26 scripts 193 downloads 5 exports 134 dependencies

Last updated from:7171963893. Checks:1 NOTE, 12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE334
linux-devel-arm64OK537
linux-devel-x86_64OK670
source / vignettesOK631
linux-release-arm64OK527
linux-release-x86_64OK610
macos-release-arm64OK334
macos-release-x86_64OK1042
macos-oldrel-arm64OK363
macos-oldrel-x86_64OK781
windows-develOK674
windows-releaseOK633
windows-oldrelOK620
wasm-releaseFAIL201

Exports:decemedipgetRoiReadCountgetSummaryOnPimakeReferencePanelplotDiagnostics

Dependencies:abindAnnotationDbiaskpassbackportsbayesplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomecachemcallrcheckmatecigarilloclicodetoolscowplotcpp11crayoncurlDBIdbplyrDelayedArraydescdistributionalDNAcopydplyredgeRfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggridgesgluegridExtragtablegtoolshmshttrhttr2inlineIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitloomagrittrMatrixMatrixGenericsmatrixStatsMEDIPSmemoisemimenumDerivopensslpillarpkgbuildpkgconfigplyrpngposteriorpreprocessCoreprettyunitsprocessxprogresspspurrrQuickJSRR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRcppParallelRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsRSQLiterstanrstantoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArrayStanHeadersstatmodstringistringrSummarizedExperimentsystensorAtibbletidyrtidyselectutf8vctrsviridisLitewithrXMLxml2XVectoryaml

Cell type deconvolutiond of (cf)MeDIP-seq data with decemedip

Ning Shen

Rendered fromhow-to-use-decemedip.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-10-06
Started: 2025-01-31

Readme and manuals

Help Manual

Help pageTopics
The 'decemedip' package.decemedip-package
Main function to perform cell type deconvolution with MeDIP-seq datadecemedip
Subset of hg19.ref.anc.se as a lightweighted exampleexample.hg19.ref.anc.se
Subset of hg19.ref.cts.se as a lightweighted exampleexample.hg19.ref.cts.se
Subset of pdx.counts.anc.se as a lightweighted exampleexample.pdx.counts.anc.se
Subset of pdx.counts.cts.se as a lightweighted exampleexample.pdx.counts.cts.se
Obtain read counts of regions of interest from MeDIP-seq bam filesgetRoiReadCount
Extract summary statistics and diagnostics on fitted cell type proportionsgetSummaryOnPi
Hg19 genomic information of anchor CpGs (i.e., all-tissue unmethylated/methylation probes) inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6). Used as default in 'decemedip'.hg19.ref.anc.se
Hg19 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).hg19.ref.cts.se
Hg38 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).hg38.ref.anc.se
Hg38 genomic information of cell-type-specific marker CpGs inferred from DNA methylation atlas published by Moss 2018 Nat. Commun. (https://www.nature.com/articles/s41467-018-07466-6).hg38.ref.cts.se
Function for assembling a SummarizedExperiment object of reference panel in *hg19* for cell type deconvolution (which is used in 'decemedip' function)makeReferencePanel
MeDIP-seq read counts on reference anchor CpGs of 3 PDX samples from Berchuck et al. 2022pdx.counts.anc.se
MeDIP-seq read counts on reference cell type-specific CpGs of 3 PDX samples from Berchuck et al. 2022pdx.counts.cts.se
Diagnostics for model fitting in 'decemedip()'plotDiagnostics