title: "HarmanData: example and reference data to use with batch correction package Harman"author: "Jason Ross and Yalchin Oytam"date: "r doc_date()"package: "r pkg_ver('HarmanData')"output:BiocStyle::html_documentvignette: >%\VignetteIndexEntry | Overview | Example gene expression data | IMR90 | NPM | OLF | Usage | Methylation reference data | Infinium5 | episcope | References
Package: HarmanData 1.41.0
Jason Ross
HarmanData: Data for the Harman package
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.
Authors:
HarmanData_1.41.0.tar.gz
HarmanData_1.41.0.tar.gz(r-4.7-any)HarmanData_1.41.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HarmanData/json (API)
| # Install 'HarmanData' in R: |
| install.packages('HarmanData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- episcope - Infinium Methylation BeadChip batch correction reference data
- imr90.data - IMR90 data, a Human lung fibroblast cell line.
- imr90.info - IMR90 data, a Human lung fibroblast cell line.
- lvr.combat - Infinium Methylation BeadChip batch correction reference data
- lvr.harman - Infinium Methylation BeadChip batch correction reference data
- md.combat - Infinium Methylation BeadChip batch correction reference data
- md.harman - Infinium Methylation BeadChip batch correction reference data
- npm.data - Non-pregant mice study data
- npm.info - Non-pregant mice study data
- olf.data - Olfactory stem cell study data
- olf.info - Olfactory stem cell study data
On BioConductor:HarmanData-1.41.0(data/experiment 3.24)HarmanData-1.40.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
expressiondatamicroarraydataexperimentdatahomo_sapiens_datamus_musculus_datadatapkg
Last updated from:db17fbf821. Checks:1 ERROR, 3 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 142 | ||
| linux-devel | OK | 228 | ||
| source / vignettes | OK | 220 | ||
| linux-release | OK | 177 |
Exports:
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Infinium Methylation BeadChip batch correction reference data | episcope |
| IMR90 data, a Human lung fibroblast cell line. | IMR90 imr90.data imr90.info |
| Infinium Methylation BeadChip batch correction reference data | Infinium5 lvr.combat lvr.harman md.combat md.harman |
| Non-pregant mice study data | NPM npm.data npm.info |
| Olfactory stem cell study data | OLF olf.data olf.info |