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panp

Presence-Absence Calls from Negative Strand Matching Probesets


Bioconductor version: Release (3.18)

A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

Author: Peter Warren

Maintainer: Peter Warren <peter.warren at verizon.net>

Citation (from within R, enter citation("panp")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("panp")

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("panp")
gene presence/absence calls PDF R Script
Reference Manual PDF

Details

biocViews Infrastructure, Software
Version 1.72.0
In Bioconductor since BioC 1.8 (R-2.3) (18 years)
License GPL (>= 2)
Depends R (>= 2.10), affy(>= 1.23.4), Biobase(>= 2.5.5)
Imports Biobase, methods, stats, utils
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package panp_1.72.0.tar.gz
Windows Binary panp_1.72.0.zip
macOS Binary (x86_64) panp_1.72.0.tgz
macOS Binary (arm64) panp_1.72.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/panp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/panp
Bioc Package Browser https://code.bioconductor.org/browse/panp/
Package Short Url https://bioconductor.org/packages/panp/
Package Downloads Report Download Stats