SCAN.UPC
This is the development version of SCAN.UPC; for the stable release version, see SCAN.UPC.
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Bioconductor version: Development (3.24)
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")):
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("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 | 2.55.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 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 |
| System Requirements | |
| URL | http://bioconductor.org http://jlab.bu.edu/software/scan-upc |
See More
| Suggests | pd.hg.u95a |
| 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 | SCAN.UPC_2.55.0.tar.gz |
| Windows Binary (x86_64) | SCAN.UPC_2.55.0.zip |
| macOS Binary (big-sur-x86_64) | SCAN.UPC_2.55.0.tgz |
| macOS Binary (sonoma-arm64) | SCAN.UPC_2.55.0.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 |