panp
This is the released version of panp; for the devel version, see panp.
All Bioconductor versions of panp
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5
Presence-Absence Calls from Negative Strand Matching Probesets
Bioconductor version: 3.23 · Package version: 1.82.0
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"):
Peter Warren. panp: Presence-Absence Calls from Negative Strand Matching Probesets. doi:10.18129/B9.bioc.panp, R package version 1.82.0, https://bioconductor.org/packages/panp.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.82.0 |
| License | GPL (>= 2) |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.5 or earlier (R-2.10) (16 years) |
| Downloads rank | 552 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Infrastructure, Software |
| Package Short Url | https://bioconductor.org/packages/panp/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("panp")| gene presence/absence calls | R Script | |
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | panp_1.82.0.tar.gz |
| Windows binary (x86_64) | panp_1.82.0.zip |
| macOS binary (arm64) | panp_1.82.0.tgz |
| macOS binary (x86_64) | panp_1.82.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/panp |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/panp |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 2.10), affy (>= 1.23.4), Biobase (>= 2.5.5)
Imports: Biobase, methods, stats, utils
Suggests: gcrma