# Transcriptome instability analysis

## Documentation for package ‘TIN’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aberrantExonUsage | Calculations of relative aberrant exon usage amounts per sample (based on FIRMA scores)
clusterPlot | clusterPlot
correlation | Calculates the correlation between sample-wise amounts of aberrant exon usage and splicing factor expression levels
correlationPlot | correlationPlot
firmaAnalysis | Read CEL files and perform FIRMA analysis
geneAnnotation | geneAnnotation
geneSetCorrelation | Correlation between aberrant exon usage and expression levels for a number of gene sets.
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 per sample
splicingFactors | A list of 280 splicing factor genes