Package: GeneRegionScan 1.63.0

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:Lasse Folkersen, Diego Diez

GeneRegionScan_1.63.0.tar.gz
GeneRegionScan_1.63.0.zip(r-4.5)GeneRegionScan_1.63.0.zip(r-4.4)GeneRegionScan_1.63.0.zip(r-4.3)
GeneRegionScan_1.63.0.tgz(r-4.4-any)GeneRegionScan_1.63.0.tgz(r-4.3-any)
GeneRegionScan_1.63.0.tar.gz(r-4.5-noble)GeneRegionScan_1.63.0.tar.gz(r-4.4-noble)
GeneRegionScan_1.63.0.tgz(r-4.4-emscripten)GeneRegionScan_1.63.0.tgz(r-4.3-emscripten)
GeneRegionScan.pdf |GeneRegionScan.html✨
GeneRegionScan/json (API)

# Install 'GeneRegionScan' in R:
install.packages('GeneRegionScan', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • exampleProbeLevelSet - Example Dataset of class 'ProbeLevelSet'
  • genomic - Genomic sequence of gene in ProbeLevelSet
  • mrna - MRNA sequence of gene in ProbeLevelSet

On BioConductor:GeneRegionScan-1.63.0(bioc 3.21)GeneRegionScan-1.62.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarraydataimportsnponechannelvisualization

3.78 score 1 scripts 290 downloads 3 mentions 16 exports 22 dependencies

Last updated 23 days agofrom:1cf7743d6c. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winWARNINGNov 08 2024
R-4.5-linuxWARNINGNov 08 2024
R-4.4-winWARNINGNov 08 2024
R-4.4-macNOTENov 08 2024
R-4.3-winWARNINGNov 08 2024
R-4.3-macNOTENov 08 2024

Exports:addSnpPdataexcludeDoubleMatchingProbesexonStructurefindProbePositionsfindSequenceInGenomegeneRegionScangetLocalMetaprobeIntensitiesgetLocalProbeIntensitiesgetMetaprobesetsFromRegionOfInterestgetProbesetsFromMetaprobesetgetProbesetsFromRegionOfInterestgetSequencegetServerProbeIntensitiesplotCoexpressionplotOnGenetranslateSampleNames

Dependencies:affxparseraskpassBiobaseBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6RColorBrewerS4VectorssysUCSC.utilsXVectorzlibbioc

GeneRegionScan

Rendered fromGeneRegionScan.Rnwusingutils::Sweaveon Nov 08 2024.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Add SNP data from hapmap-style data file to pData of ExpressionSetaddSnpPdata addSnpPdata,ExpressionSet-method
Check For File In PathcheckForFileInPath
Do Probe LineardoProbeLinear
Do Probe T-TestdoProbeTTest
Example Dataset of class 'ProbeLevelSet'exampleProbeLevelSet
Exclude ProbeLevelSet probes that match more than once in genomeexcludeDoubleMatchingProbes excludeDoubleMatchingProbes,ProbeLevelSet-method
Add exon-structure to plotsexonStructure
Find positions of probes on a genefindProbePositions findProbePositions,ExpressionSet-method
Find a sequence in genomefindSequenceInGenome
Gene Region ScanGeneRegionScan geneRegionScan geneRegionScan,ExpressionSet-method
genomic sequence of gene in ProbeLevelSetgenomic
Get Metaprobe Intensities locallygetLocalMetaprobeIntensities
Get Probe Intensities locallygetLocalProbeIntensities
Get Meta Probe Set IDs From Region Of InterestgetMetaprobesetsFromRegionOfInterest
Get ProbeLevel Annotation for Exon ArraysgetProbeLevelAnnotationForExonArrays
Get Probeset IDs From metaprobeset IDsgetProbesetsFromMetaprobeset
Get Probeset IDs From Region Of InterestgetProbesetsFromRegionOfInterest
Get Sequence from a ProbeLevelSetgetSequence getSequence,ProbeLevelSet-method
Get Probe Intensities from a servergetServerProbeIntensities
mRNA sequence of gene in ProbeLevelSetmrna
Plot Coexpression of probes in a ProbeLevelSetplotCoexpression plotCoexpression,ExpressionSet-method
Plot probe level data on a geneplotOnGene plotOnGene,ExpressionSet-method
Plot StatisticsplotStatistics
Class ProbeLevelSetProbeLevelSet ProbeLevelSet-class
Standardize reading of gene inputsreadGeneInput
Translate sample names using translation filetranslateSampleNames translateSampleNames,ExpressionSet-method