tRanslatome: Comparison between multiple levels of gene expression

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, SAM, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.

AuthorToma Tebaldi, Erik Dassi, Galena Kostoska
Date of publicationNone
MaintainerToma Tebaldi <tebaldi@science.unitn.it>, Erik Dassi <erik.dassi@unitn.it>
LicenseGPL-3
Version1.12.0

View on Bioconductor

Man pages

average.similarity.scores: labelLevelsGOSetsHelpfile

computeDEGs: computeDEGsHelpfile

CVplot: CVplotDEGsHelpfile

DEGs: Class 'DEGs'

DEGs.table: DEGsTableDEGsHelpfile

EnrichedSets: Class 'EnrichedSets'

enriched.table: enrichedtableenrichedSetsHelpfile

FC.threshold: FCThresholdDEGsHelpfile

getConditionA: getConditionATranslatomeDatasetHelpfile

getConditionB: getConditionBTranslatomeDatasetHelpfile

getConditionC: getConditionCTranslatomeDatasetHelpfile

getConditionD: getConditionDTranslatomeDatasetHelpfile

getConditionLabels: getConditionLabelsTranslatomeDatasetHelpfile

getDataType: getDataTypeTranslatomeDatasetHelpfile

getDEGs: getDEGsTranslatomeDatasetHelpfile

getDEGsMethod: getDEGsMethodDEGsHelpfile

getExprMatrix: getExprMatrixTranslatomeDatasetHelpfile

getLevelLabels: getLevelLabelsTranslatomeDatasetHelpfile

GOComparison: GOComparisonHelpfile

GOEnrichment: GOEnrichmentHelpfile

GOsets: Class 'GOsets'

GOsims: Class 'GOsims'

Heatmap: HeatmapEnrichedHelpfile

Histogram: HistogramHelpfile

identity.matrix: labelLevelsGOSetsHelpfile

IdentityPlot: IdentityPlotHelpfile

label.condition: labelConditionDEGsHelpfile

label.level.DEGs: labelLevelDEGsHelpfile

label.level.enriched: labelLevelsEnrichedSetsHelpfile

MAplot: MAplotHelpfile

newTranslatomeDataset: newTranslatomeDatasetHelpfile

Radar: RadarEnrichedHelpfile

RegulatoryEnrichment: RegulatoryEnrichmentHelpfile

Scatterplot: ScatterplotHelpfile

SDplot: SDplotHelpfile

significance.threshold: significanceThresholdDEGsHelpfile

similarity.matrix: similaritymatrixGOSetsHelpfile

SimilarityPlot: SimilarityPlotHelpfile

TranslatomeDataset: Class 'TranslatomeDataset'

tRanslatome-package: tRanslatome

tRanslatomeSampleData: Sample data set for tRanslatome

Files in this package

tRanslatome/DESCRIPTION
tRanslatome/NAMESPACE
tRanslatome/R
tRanslatome/R/DEGs.R tRanslatome/R/EnrichedSets.R tRanslatome/R/GOsets.R tRanslatome/R/GOsims.R tRanslatome/R/TranslatomeDataset.R
tRanslatome/build
tRanslatome/build/vignette.rds
tRanslatome/data
tRanslatome/data/tRanslatomeSampleData.RData
tRanslatome/inst
tRanslatome/inst/doc
tRanslatome/inst/doc/tRanslatome_package.R
tRanslatome/inst/doc/tRanslatome_package.Rnw
tRanslatome/inst/doc/tRanslatome_package.pdf
tRanslatome/man
tRanslatome/man/CVplot.Rd tRanslatome/man/DEGs.Rd tRanslatome/man/DEGs.table.Rd tRanslatome/man/EnrichedSets.Rd tRanslatome/man/FC.threshold.Rd tRanslatome/man/GOComparison.Rd tRanslatome/man/GOEnrichment.Rd tRanslatome/man/GOsets.Rd tRanslatome/man/GOsims.Rd tRanslatome/man/Heatmap.Rd tRanslatome/man/Histogram.Rd tRanslatome/man/IdentityPlot.Rd tRanslatome/man/MAplot.Rd tRanslatome/man/Radar.Rd tRanslatome/man/RegulatoryEnrichment.Rd tRanslatome/man/SDplot.Rd tRanslatome/man/Scatterplot.Rd tRanslatome/man/SimilarityPlot.Rd tRanslatome/man/TranslatomeDataset.Rd tRanslatome/man/average.similarity.scores.Rd tRanslatome/man/computeDEGs.Rd tRanslatome/man/enriched.table.Rd tRanslatome/man/getConditionA.Rd tRanslatome/man/getConditionB.Rd tRanslatome/man/getConditionC.Rd tRanslatome/man/getConditionD.Rd tRanslatome/man/getConditionLabels.Rd tRanslatome/man/getDEGs.Rd tRanslatome/man/getDEGsMethod.Rd tRanslatome/man/getDataType.Rd tRanslatome/man/getExprMatrix.Rd tRanslatome/man/getLevelLabels.Rd tRanslatome/man/identity.matrix.Rd tRanslatome/man/label.condition.Rd tRanslatome/man/label.level.DEGs.Rd tRanslatome/man/label.level.enriched.Rd tRanslatome/man/newTranslatomeDataset.Rd tRanslatome/man/significance.threshold.Rd tRanslatome/man/similarity.matrix.Rd tRanslatome/man/tRanslatome-package.Rd tRanslatome/man/tRanslatomeSampleData.Rd
tRanslatome/vignettes
tRanslatome/vignettes/fig
tRanslatome/vignettes/fig/CVplot.png
tRanslatome/vignettes/fig/Heatmap.png
tRanslatome/vignettes/fig/HistogramDetailed.png
tRanslatome/vignettes/fig/HistogramSummary.png
tRanslatome/vignettes/fig/IdentityPlot.png
tRanslatome/vignettes/fig/MAplot.png
tRanslatome/vignettes/fig/Radar.png
tRanslatome/vignettes/fig/SDplot.png
tRanslatome/vignettes/fig/Scatterplot.png
tRanslatome/vignettes/fig/SimilarityPlot.png
tRanslatome/vignettes/tRanslatome_package.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.