panp

DOI: 10.18129/B9.bioc.panp    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see panp.

Presence-Absence Calls from Negative Strand Matching Probesets

Bioconductor version: 3.13

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 "4.1") and enter:

if (!requireNamespace("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")

 

PDF R Script gene presence/absence calls
PDF   Reference Manual

Details

biocViews Infrastructure, Software
Version 1.62.0
In Bioconductor since BioC 1.8 (R-2.3) (15.5 years)
License GPL (>= 2)
Depends R (>= 2.10), affy(>= 1.23.4), Biobase(>= 2.5.5)
Imports Biobase, methods, stats, utils
LinkingTo
Suggests gcrma
SystemRequirements
Enhances
URL
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 panp_1.62.0.tar.gz
Windows Binary panp_1.62.0.zip
macOS 10.13 (High Sierra) panp_1.62.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/panp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/panp
Package Short Url https://bioconductor.org/packages/panp/
Package Downloads Report Download Stats

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