Harshlight
A "corrective make-up" program for microarray chips
Bioconductor version: Release (3.20)
The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.
Author: Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco
Maintainer: Maurizio Pellegrino <mpellegri at berkeley.edu>
citation("Harshlight")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Harshlight")
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("Harshlight")| Harshlight | R Script | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software |
| Version | 1.78.0 |
| In Bioconductor since | BioC 1.9 (R-2.4) (18 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10) |
| Imports | affy, altcdfenvs, Biobase, stats, utils |
| System Requirements | |
| URL | http://asterion.rockefeller.edu/Harshlight/ |
See More
| Suggests | |
| 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 | Harshlight_1.78.0.tar.gz |
| Windows Binary (x86_64) | Harshlight_1.78.0.zip (64-bit only) |
| macOS Binary (x86_64) | Harshlight_1.78.0.tgz |
| macOS Binary (arm64) | Harshlight_1.77.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Harshlight |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Harshlight |
| Bioc Package Browser | https://code.bioconductor.org/browse/Harshlight/ |
| Package Short Url | https://bioconductor.org/packages/Harshlight/ |
| Package Downloads Report | Download Stats |