SCAN.UPC
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Bioconductor version: Release (3.17)
SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.
Author: Stephen R. Piccolo and Andrea H. Bild and W. Evan Johnson
Maintainer: Stephen R. Piccolo <stephen_piccolo at byu.edu>
citation("SCAN.UPC")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SCAN.UPC")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("SCAN.UPC")| Primer | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, Microarray, OneChannel, Preprocessing, RNASeq, Software, TwoChannel |
| Version | 2.42.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11 years) |
| License | MIT |
| Depends | R (>= 2.14.0), Biobase(>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva |
| Imports | utils, methods, MASS, tools, IRanges |
| Linking To | |
| Suggests | pd.hg.u95a |
| System Requirements | |
| Enhances | |
| URL | http://bioconductor.org http://jlab.bu.edu/software/scan-upc |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SCAN.UPC_2.42.0.tar.gz |
| Windows Binary | SCAN.UPC_2.42.0.zip |
| macOS Binary (x86_64) | SCAN.UPC_2.42.0.tgz |
| macOS Binary (arm64) | SCAN.UPC_2.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SCAN.UPC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SCAN.UPC |
| Bioc Package Browser | https://code.bioconductor.org/browse/SCAN.UPC/ |
| Package Short Url | https://bioconductor.org/packages/SCAN.UPC/ |
| Package Downloads Report | Download Stats |