panp
This is the development version of panp; for the stable release version, see panp.
Presence-Absence Calls from Negative Strand Matching Probesets
Bioconductor version: Development (3.24)
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("panp")):
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("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 | R Script | |
| Reference Manual |
Details
| biocViews | Infrastructure, Software |
| Version | 1.83.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (20.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10), affy(>= 1.23.4), Biobase(>= 2.5.5) |
| Imports | Biobase, methods, stats, utils |
| System Requirements | |
| URL |
See More
| 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_1.83.0.tar.gz |
| Windows Binary (x86_64) | panp_1.83.0.zip |
| macOS Binary (big-sur-x86_64) | panp_1.83.0.tgz |
| macOS Binary (sonoma-arm64) | panp_1.83.0.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 |