TIN: Transcriptome instability analysis
Version 1.8.0

The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.

AuthorBjarne Johannessen, Anita Sveen and Rolf I. Skotheim
Bioconductor views AlternativeSplicing DifferentialSplicing ExonArray GeneExpression Genetics Microarray
Date of publicationNone
MaintainerBjarne Johannessen <bjajoh@rr-research.no>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("TIN")

Popular man pages

clusterPlot: clusterPlot
correlation: Calculates the correlation between sample-wise amounts of...
correlationPlot: correlationPlot
geneSetCorrelation: Correlation between aberrant exon usage and expression levels...
probesetPermutations: Permutations of the samples at each probeset
scatterPlot: Scatterplot showing relative amounts of aberrant exon usage...
splicingFactors: A list of 280 splicing factor genes
See all...

All man pages Function index File listing

Man pages

aberrantExonUsage: Calculations of relative aberrant exon usage amounts per...
clusterPlot: clusterPlot
correlation: Calculates the correlation between sample-wise amounts of...
correlationPlot: correlationPlot
firmaAnalysis: Read CEL files and perform FIRMA analysis
geneAnnotation: geneAnnotation
geneSetCorrelation: Correlation between aberrant exon usage and expression levels...
geneSets: geneSets
posNegCorrPlot: posNegCorrPlot
probesetPermutations: Permutations of the samples at each probeset
readGeneSummaries: Read gene-level expression summaries
sampleSetFirmaScores: sampleSetFirmaScores
sampleSetGeneSummaries: sampleSetGeneSummaries
scatterPlot: Scatterplot showing relative amounts of aberrant exon usage...
splicingFactors: A list of 280 splicing factor genes

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/aberrantExonUsage.R
R/clusterPlot.R
R/correlation.R
R/correlationPlot.R
R/firmaAnalysis.R
R/geneSetCorrelation.R
R/posNegCorrPlot.R
R/probesetPermutations.R
R/readGeneSummaries.R
R/scatterPlot.R
build
build/vignette.rds
data
data/datalist
data/geneAnnotation.rda
data/geneSets.rda
data/sampleSetFirmaScores.rda
data/sampleSetGeneSummaries.rda
data/splicingFactors.rda
doc
doc/TIN.pdf
inst
inst/doc
inst/doc/TIN.R
inst/doc/TIN.Rnw
inst/doc/TIN.pdf
inst/unitTests
inst/unitTests/test_aberrantExonUsage.R
inst/unitTests/test_firmaAnalysis.R
inst/unitTests/test_geneSetCorrelation.R
inst/unitTests/test_probesetPermutations.R
inst/unitTests/test_readGeneSummaries.R
man
man/aberrantExonUsage.Rd
man/clusterPlot.Rd
man/correlation.Rd
man/correlationPlot.Rd
man/firmaAnalysis.Rd
man/geneAnnotation.Rd
man/geneSetCorrelation.Rd
man/geneSets.Rd
man/posNegCorrPlot.Rd
man/probesetPermutations.Rd
man/readGeneSummaries.Rd
man/sampleSetFirmaScores.Rd
man/sampleSetGeneSummaries.Rd
man/scatterPlot.Rd
man/splicingFactors.Rd
tests
tests/runTests.R
vignettes
vignettes/TIN.Rnw
TIN documentation built on May 20, 2017, 9:16 p.m.

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