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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decemedip_1.1.0.tgz(r-4.6-x86_64)decemedip_1.1.0.tgz(r-4.6-arm64)decemedip_1.1.0.tgz(r-4.5-x86_64)decemedip_1.1.0.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
decemedip/json (API)

# 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)

software immunooncology dnamethylation epigenetics sequencing wholegenome bayesian bayesian-data-analysis bayesian-inference bioinformatics dna-methylation dna-methylation-data epigenomics generative-model omics rstan stan cpp

5.41 score 4 stars 43 scripts 5 exports 135 dependencies

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

Target	Result	Time
bioc-checks	NOTE	343
linux-devel-arm64	OK	558
linux-devel-x86_64	OK	693
source / vignettes	OK	632
linux-release-arm64	OK	562
linux-release-x86_64	OK	646
macos-release-arm64	OK	466
macos-release-x86_64	OK	687
macos-oldrel-arm64	OK	288
macos-oldrel-x86_64	OK	749
windows-devel	OK	630
windows-release	OK	632
windows-oldrel	OK	607
wasm-release	FAIL	244

Exports:decemedip getRoiReadCount getSummaryOnPi makeReferencePanel plotDiagnostics

Dependencies:abind AnnotationDbi askpass backports bayesplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem callr checkmate cigarillo cli codetools cowplot cpp11 crayon curl DBI dbplyr DelayedArray desc distributional DNAcopy dplyr edgeR farver fastmap filelock formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 ggridges glue gridExtra gtable gtools hms httr httr2 inline IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit loo magrittr Matrix MatrixGenerics matrixStats MEDIPS memoise mime numDeriv openssl otel pillar pkgbuild pkgconfig plyr png posterior preprocessCore prettyunits processx progress ps purrr QuickJSR R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RcppParallel RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools RSQLite rstan rstantools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray StanHeaders statmod stringi stringr SummarizedExperiment sys tensorA tibble tidyr tidyselect utf8 vctrs viridisLite withr XML xml2 XVector yaml

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

Rendered fromhow-to-use-decemedip.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The 'decemedip' package.	decemedip-package
Main function to perform cell type deconvolution with MeDIP-seq data	decemedip
Subset of hg19.ref.anc.se as a lightweighted example	example.hg19.ref.anc.se
Subset of hg19.ref.cts.se as a lightweighted example	example.hg19.ref.cts.se
Subset of pdx.counts.anc.se as a lightweighted example	example.pdx.counts.anc.se
Subset of pdx.counts.cts.se as a lightweighted example	example.pdx.counts.cts.se
Obtain read counts of regions of interest from MeDIP-seq bam files	getRoiReadCount
Extract summary statistics and diagnostics on fitted cell type proportions	getSummaryOnPi
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. 2022	pdx.counts.anc.se
MeDIP-seq read counts on reference cell type-specific CpGs of 3 PDX samples from Berchuck et al. 2022	pdx.counts.cts.se
Diagnostics for model fitting in 'decemedip()'	plotDiagnostics