Example of building a ProbeLevelSet | Example of using a ProbeLevelSet
Package: GeneRegionScan 1.69.0
Lasse Folkersen
GeneRegionScan: GeneRegionScan
A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.
Authors:
GeneRegionScan_1.69.0.tar.gz
GeneRegionScan_1.69.0.zip(r-4.7)GeneRegionScan_1.69.0.zip(r-4.6)GeneRegionScan_1.69.0.zip(r-4.5)
GeneRegionScan_1.69.0.tgz(r-4.6-any)GeneRegionScan_1.69.0.tgz(r-4.5-any)
GeneRegionScan_1.69.0.tar.gz(r-4.7-any)GeneRegionScan_1.69.0.tar.gz(r-4.6-any)
GeneRegionScan_1.69.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GeneRegionScan/json (API)
| # Install 'GeneRegionScan' in R: |
| install.packages('GeneRegionScan', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- exampleProbeLevelSet - Example Dataset of class 'ProbeLevelSet'
- genomic - Genomic sequence of gene in ProbeLevelSet
- mrna - MRNA sequence of gene in ProbeLevelSet
On BioConductor:GeneRegionScan-1.69.0(bioc 3.24)GeneRegionScan-1.68.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraydataimportsnponechannelvisualization
Last updated from:4cb621e131. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 168 | ||
| linux-devel-x86_64 | NOTE | 246 | ||
| source / vignettes | OK | 225 | ||
| linux-release-x86_64 | NOTE | 246 | ||
| macos-release-arm64 | NOTE | 119 | ||
| macos-oldrel-arm64 | NOTE | 112 | ||
| windows-devel | NOTE | 186 | ||
| windows-release | NOTE | 167 | ||
| windows-oldrel | NOTE | 150 | ||
| wasm-release | OK | 143 |
Exports:addSnpPdataexcludeDoubleMatchingProbesexonStructurefindProbePositionsfindSequenceInGenomegeneRegionScangetLocalMetaprobeIntensitiesgetLocalProbeIntensitiesgetMetaprobesetsFromRegionOfInterestgetProbesetsFromMetaprobesetgetProbesetsFromRegionOfInterestgetSequencegetServerProbeIntensitiesplotCoexpressionplotOnGenetranslateSampleNames
Dependencies:affxparserBiobaseBiocGenericsBiostringscrayongenericsIRangesRColorBrewerS4VectorsSeqinfoXVector
