Background | Preprocessing CEL file data for panp | Creating gene detection calls with panp | Extracting P/M/A calls and p-values | Illustrating panp's decisions | References
Package: panp 1.83.0
Peter Warren
panp: Presence-Absence Calls from Negative Strand Matching Probesets
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.
Authors:
panp_1.83.0.tar.gz
panp_1.83.0.zip(r-4.7)panp_1.83.0.zip(r-4.6)panp_1.83.0.zip(r-4.5)
panp_1.83.0.tgz(r-4.6-any)panp_1.83.0.tgz(r-4.5-any)
panp_1.83.0.tar.gz(r-4.7-any)panp_1.83.0.tar.gz(r-4.6-any)
panp_1.83.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
panp/json (API)
| # Install 'panp' in R: |
| install.packages('panp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- gcrma.ExpressionSet - ExpressionSet resulting from gcrma processing of 3 HG-U133A chips
- NSMPnames.hgu133a - Negative Strand Matching Probeset (NSMP) names for HG-U133A chip type
- NSMPnames.hgu133plus2 - Negative Strand Matching Probeset (NSMP) names for HG-U133 Plus 2.0 chip type
On BioConductor:panp-1.83.0(bioc 3.24)panp-1.82.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:ff4c58cac6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 191 | ||
| linux-devel-x86_64 | NOTE | 140 | ||
| source / vignettes | OK | 163 | ||
| linux-release-x86_64 | NOTE | 160 | ||
| macos-release-arm64 | NOTE | 78 | ||
| macos-oldrel-arm64 | NOTE | 77 | ||
| windows-devel | NOTE | 79 | ||
| windows-release | NOTE | 88 | ||
| windows-oldrel | NOTE | 85 | ||
| wasm-release | OK | 104 |
Exports:pa.calls
Dependencies:affyaffyioBiobaseBiocGenericsBiocManagergenericspreprocessCore
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ExpressionSet resulting from gcrma processing of 3 HG-U133A chips | gcrma.ExpressionSet |
| Negative Strand Matching Probeset (NSMP) names for HG-U133A chip type | NSMPnames.hgu133a |
| Negative Strand Matching Probeset (NSMP) names for HG-U133 Plus 2.0 chip type | NSMPnames.hgu133plus2 |
| Presence-Absence Calls from Negative Strand Matching Probesets | pa.calls |