panp

Presence-Absence Calls from Negative Strand Matching Probesets

Bioconductor version: Release (3.20)

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, Software
Version	1.76.0
In Bioconductor since	BioC 1.8 (R-2.3) (18.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10), affy(>= 1.23.4), Biobase(>= 2.5.5)
Imports	Biobase, methods, stats, utils
System Requirements
URL

Suggests	gcrma
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	panp_1.76.0.tar.gz
Windows Binary (x86_64)	panp_1.76.0.zip
macOS Binary (x86_64)	panp_1.76.0.tgz
macOS Binary (arm64)	panp_1.76.0.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