TIN: Transcriptome instability analysis

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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.

Author
Bjarne Johannessen, Anita Sveen and Rolf I. Skotheim
Date of publication
None
Maintainer
Bjarne Johannessen <bjajoh@rr-research.no>
License
Artistic-2.0
Version
1.6.0

View on Bioconductor

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

Files in this package

TIN/DESCRIPTION
TIN/NAMESPACE
TIN/NEWS
TIN/R
TIN/R/aberrantExonUsage.R
TIN/R/clusterPlot.R
TIN/R/correlation.R
TIN/R/correlationPlot.R
TIN/R/firmaAnalysis.R
TIN/R/geneSetCorrelation.R
TIN/R/posNegCorrPlot.R
TIN/R/probesetPermutations.R
TIN/R/readGeneSummaries.R
TIN/R/scatterPlot.R
TIN/build
TIN/build/vignette.rds
TIN/data
TIN/data/datalist
TIN/data/geneAnnotation.rda
TIN/data/geneSets.rda
TIN/data/sampleSetFirmaScores.rda
TIN/data/sampleSetGeneSummaries.rda
TIN/data/splicingFactors.rda
TIN/doc
TIN/doc/TIN.pdf
TIN/inst
TIN/inst/doc
TIN/inst/doc/TIN.R
TIN/inst/doc/TIN.Rnw
TIN/inst/doc/TIN.pdf
TIN/inst/unitTests
TIN/inst/unitTests/test_aberrantExonUsage.R
TIN/inst/unitTests/test_firmaAnalysis.R
TIN/inst/unitTests/test_geneSetCorrelation.R
TIN/inst/unitTests/test_probesetPermutations.R
TIN/inst/unitTests/test_readGeneSummaries.R
TIN/man
TIN/man/aberrantExonUsage.Rd
TIN/man/clusterPlot.Rd
TIN/man/correlation.Rd
TIN/man/correlationPlot.Rd
TIN/man/firmaAnalysis.Rd
TIN/man/geneAnnotation.Rd
TIN/man/geneSetCorrelation.Rd
TIN/man/geneSets.Rd
TIN/man/posNegCorrPlot.Rd
TIN/man/probesetPermutations.Rd
TIN/man/readGeneSummaries.Rd
TIN/man/sampleSetFirmaScores.Rd
TIN/man/sampleSetGeneSummaries.Rd
TIN/man/scatterPlot.Rd
TIN/man/splicingFactors.Rd
TIN/tests
TIN/tests/runTests.R
TIN/vignettes
TIN/vignettes/TIN.Rnw