Package: TIN 1.39.0
Bjarne Johannessen
TIN: Transcriptome instability analysis
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.
Authors:
TIN_1.39.0.tar.gz
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TIN_1.39.0.tgz(r-4.4-any)TIN_1.39.0.tgz(r-4.3-any)
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TIN_1.39.0.tgz(r-4.4-emscripten)TIN_1.39.0.tgz(r-4.3-emscripten)
TIN.pdf |TIN.html✨
TIN/json (API)
NEWS
| # Install 'TIN' in R: |
| install.packages('TIN', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- geneAnnotation - GeneAnnotation
- geneSets - GeneSets
- sampleSetFirmaScores - SampleSetFirmaScores
- sampleSetGeneSummaries - SampleSetGeneSummaries
- splicingFactors - A list of 280 splicing factor genes
On BioConductor:TIN-1.39.0(bioc 3.21)TIN-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
exonarraymicroarraygeneexpressionalternativesplicinggeneticsdifferentialsplicing
Last updated 23 days agofrom:6ae7ba4949. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:aberrantExonUsageclusterPlotcorrelationcorrelationPlotfirmaAnalysisgeneSetCorrelationposNegCorrPlotprobesetPermutationsreadGeneSummariesscatterPlot
Dependencies:AnnotationDbiaroma.affymetrixaroma.apdaroma.corearoma.lightaskpassbackportsbase64encBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdigestDNAcopydoParalleldynamicTreeCutevaluatefansifarverfastclusterfastmapfontawesomeforeachforeignFormulafsfuturegenericsGenomeInfoDbGenomeInfoDbDataggplot2globalsglueGO.dbgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrimputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglatticelifecyclelistenvmagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmennetopensslparallellypillarpkgconfigplogrpngpreprocessCorePSCBSR.cacheR.devicesR.filesetsR.hugeR.methodsS3R.ooR.rspR.utilsR6rappdirsRColorBrewerRcpprlangrmarkdownrpartRSQLiterstudioapiS4VectorssassscalessquashstringistringrsurvivalsystibbletinytexUCSC.utilsutf8vctrsviridisviridisLiteWGCNAwithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculations of relative aberrant exon usage amounts per sample (based on FIRMA scores) | aberrantExonUsage |
| clusterPlot | clusterPlot |
| Calculates the correlation between sample-wise amounts of aberrant exon usage and splicing factor expression levels | correlation |
| correlationPlot | correlationPlot |
| Read CEL files and perform FIRMA analysis | firmaAnalysis |
| geneAnnotation | geneAnnotation |
| Correlation between aberrant exon usage and expression levels for a number of gene sets. | geneSetCorrelation |
| geneSets | geneSets |
| posNegCorrPlot | posNegCorrPlot |
| Permutations of the samples at each probeset | probesetPermutations |
| Read gene-level expression summaries | readGeneSummaries |
| sampleSetFirmaScores | sampleSetFirmaScores |
| sampleSetGeneSummaries | sampleSetGeneSummaries |
| Scatterplot showing relative amounts of aberrant exon usage per sample | scatterPlot |
| A list of 280 splicing factor genes | splicingFactors |