spiky
This is the released version of spiky; for the devel version, see spiky.
All Bioconductor versions of spiky
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
Spike-in calibration for cell-free MeDIP
Bioconductor version: 3.23 · Package version: 1.18.0
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 gmail.com>
Citation
From within R, enter citation("spiky"):
Samantha Wilson, Lauren Harmon, Tim Triche. spiky: Spike-in calibration for cell-free MeDIP. doi:10.18129/B9.bioc.spiky, R package version 1.18.0, https://bioconductor.org/packages/spiky.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spiky")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.18.0 |
| License | GPL-2 |
| URL | https://github.com/trichelab/spiky |
| Bug Reports | https://github.com/trichelab/spiky/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 1818 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/spiky/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("spiky")| Spiky: Analysing cfMeDIP-seq data with spike-in controls | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | spiky_1.18.0.tar.gz |
| Windows binary (x86_64) | spiky_1.18.0.zip |
| macOS binary (arm64) | spiky_1.18.0.tgz |
| macOS binary (x86_64) | spiky_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spiky |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spiky |
| Package Downloads Report | Download Stats |
Dependencies
Depends: Rsamtools, GenomicRanges, R (>= 3.6.0)
Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils
Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager