spiky

DOI: 10.18129/B9.bioc.spiky    

This is the development version of spiky; to use it, please install the devel version of Bioconductor.

Spike-in calibration for cell-free MeDIP

Bioconductor version: Development (3.14)

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], Jordan Veldboom [ctb], 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 "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software
Version 0.99.999
In Bioconductor since BioC 3.14 (R-4.1)
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
LinkingTo
Suggests covr, testthat, equatiomatic, universalmotif, kebabs, ComplexHeatmap, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
SystemRequirements
Enhances
URL https://github.com/trichelab/spiky
BugReports https://github.com/trichelab/spiky/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package spiky_0.99.999.tar.gz
Windows Binary spiky_0.99.999.zip
macOS 10.13 (High Sierra) spiky_0.99.999.tgz
Source Repository git clone https://git.bioconductor.org/packages/spiky
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/spiky
Package Short Url https://bioconductor.org/packages/spiky/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: