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spiky

This is the development version of spiky; for the stable release version, see spiky.

Spike-in calibration for cell-free MeDIP


Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("spiky")

For older versions of R, please refer to the appropriate Bioconductor release.

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 PDF
NEWS Text

Details

biocViews DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software
Version 1.9.0
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
System Requirements
URL https://github.com/trichelab/spiky
Bug Reports https://github.com/trichelab/spiky/issues
See More
Suggests covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package spiky_1.9.0.tar.gz
Windows Binary spiky_1.9.0.zip
macOS Binary (x86_64) spiky_1.9.0.tgz
macOS Binary (arm64) spiky_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/spiky
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spiky
Bioc Package Browser https://code.bioconductor.org/browse/spiky/
Package Short Url https://bioconductor.org/packages/spiky/
Package Downloads Report Download Stats