To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Harman")
In most cases, you don't need to download the package archive at all.
Harman
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see Harman.
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Bioconductor version: 3.3
Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.
Author: Josh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut]
Maintainer: Jason Ross <jason.ross at csiro.au>
Citation (from within R,
enter citation("Harman")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Harman")
Documentation
| HTML | R Script | IntroductionToHarman |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BatchEffect, DNAMethylation, Microarray, MultipleComparison, Normalization, Preprocessing, PrincipalComponent, Software, StatisticalMethod, Transcription |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| License | GPL-3 + file LICENCE |
| Depends | R (>= 3.3) |
| Imports | Rcpp (>= 0.11.2) |
| LinkingTo | Rcpp |
| Suggests | HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, missMethyl, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData |
| SystemRequirements | |
| Enhances | |
| URL | http://www.bioinformatics.csiro.au/harman/ |
| BugReports | https://github.com/JasonR055/Harman/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Harman_1.0.2.tar.gz |
| Windows Binary | Harman_1.0.2.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | Harman_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/Harman/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/Harman/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
