HarmanData
This is the development version of HarmanData; for the stable release version, see HarmanData.
Data for the Harman package
Bioconductor version: Development (3.24)
Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three example datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles. Since version 1.24, this package also contains the Infinium5 dataset, a set of batch correction adjustments across 5 Illumina Infinium Methylation BeadChip datasets. This file does not contain methylation data, but summary statistics of 5 datasets after correction. There is also an EpiSCOPE_sample file as exampling for the new methylation clustering functionality in Harman.
Author: Yalchin Oytam [aut], Josh Bowden [aut], Jason Ross [aut, cre]
Maintainer: Jason Ross <jason.ross at csiro.au>
citation("HarmanData")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("HarmanData")
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("HarmanData")| HarmanData | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExpressionData, Homo_sapiens_Data, MicroarrayData, Mus_musculus_Data |
| Version | 1.41.0 |
| License | GPL-3 |
| Depends | R (>= 3.5.0) |
| Imports | |
| System Requirements | |
| URL | http://www.bioinformatics.csiro.au/harman/ |
See More
| Suggests | BiocGenerics, BiocStyle, knitr, rmarkdown, Harman(>= 1.23.3) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | Harman |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HarmanData_1.41.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HarmanData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HarmanData |
| Package Short Url | https://bioconductor.org/packages/HarmanData/ |
| Package Downloads Report | Download Stats |