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Spike-in calibration for cell-free MeDIP

Bioconductor version: Release (3.19)

spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.

Author: Samantha Wilson [aut], Lauren Harmon [aut], Tim Triche [aut, cre]

Maintainer: Tim Triche <trichelab at>

Citation (from within R, enter citation("spiky")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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To view documentation for the version of this package installed in your system, start R and enter:

Spiky: Analysing cfMeDIP-seq data with spike-in controls HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-2
Depends Rsamtools, GenomicRanges, R (>= 3.6.0)
Imports stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils
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Suggests covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
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Source Package spiky_1.10.0.tar.gz
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