omicsPrint
This is the released version of omicsPrint; for the devel version, see omicsPrint.
Cross omic genetic fingerprinting
Bioconductor version: Release (3.23)
omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).
Author: Maarten van Iterson [aut], Davy Cats [cre]
Maintainer: Davy Cats <davycats.dc at gmail.com>
citation("omicsPrint")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("omicsPrint")
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("omicsPrint")| omicsPrint: detection of data linkage errors in multiple omics studies | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Epigenetics, GeneticVariability, Genetics, ImmunoOncology, QualityControl, Software, Transcription, Transcriptomics |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5), MASS |
| Imports | methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | omicsPrint_1.32.0.tar.gz |
| Windows Binary (x86_64) | omicsPrint_1.32.0.zip |
| macOS Binary (big-sur-x86_64) | omicsPrint_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | omicsPrint_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/omicsPrint |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/omicsPrint |
| Bioc Package Browser | https://code.bioconductor.org/browse/omicsPrint/ |
| Package Short Url | https://bioconductor.org/packages/omicsPrint/ |
| Package Downloads Report | Download Stats |