spiky
This is thereleased version of spiky; for the devel version, seespiky.
Spike-in calibration for cell-free MeDIP
Bioconductor version: Release (3.22)
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("spiky")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("spiky")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation,DifferentialMethylation,Normalization,Preprocessing,QualityControl,Sequencing,Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | spiky_1.16.0.tar.gz |
| Windows Binary (x86_64) | spiky_1.16.0.zip |
| macOS Binary (x86_64) | spiky_1.16.0.tgz |
| macOS Binary (arm64) | spiky_1.16.0.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 |