To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("panp")
In most cases, you don't need to download the package archive at all.
panp
Presence-Absence Calls from Negative Strand Matching Probesets
Bioconductor version: 3.0
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")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("panp")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("panp")
| R Script | gene presence/absence calls | |
| Reference Manual |
Details
| biocViews | Infrastructure, Software |
| Version | 1.36.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) |
| 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | panp_1.36.0.tar.gz |
| Windows Binary | panp_1.36.0.zip |
| Mac OS X 10.6 (Snow Leopard) | panp_1.36.0.tgz |
| Mac OS X 10.9 (Mavericks) | panp_1.36.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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