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

Functions

average.similarity.scores Man page
average.similarity.scores,GOsims-method Man page
CCComparison Man page
CCEnrichment Man page
computeDEGs Man page
computeDEGs,TranslatomeDataset-method Man page
CVplot Man page
CVplot,DEGs-method Man page
DEGs-class Man page
DEGs.table Man page
DEGs.table,DEGs-method Man page
EnrichedSets-class Man page
enriched.table Man page
enriched.table,EnrichedSets-method Man page
expressionMatrix Man page
FC.threshold Man page
FC.threshold,DEGs-method Man page
getConditionA Man page
getConditionA,TranslatomeDataset-method Man page
getConditionB Man page
getConditionB,TranslatomeDataset-method Man page
getConditionC Man page
getConditionC,TranslatomeDataset-method Man page
getConditionD Man page
getConditionD,TranslatomeDataset-method Man page
getConditionLabels Man page
getConditionLabels,TranslatomeDataset-method Man page
getDataType Man page
getDataType,TranslatomeDataset-method Man page
getDEGs Man page
getDEGsMethod Man page
getDEGsMethod,DEGs-method Man page
getDEGs,TranslatomeDataset-method Man page
getExprMatrix Man page
getExprMatrix,TranslatomeDataset-method Man page
getLevelLabels Man page
getLevelLabels,TranslatomeDataset-method Man page
GOComparison Man page
GOComparison,GOsets-method Man page
GOEnrichment Man page
GOEnrichment,DEGs-method Man page
GOsets-class Man page
GOsims-class Man page
Heatmap Man page
Heatmap,EnrichedSets-method Man page
Heatmap,GOsets-method Man page
Histogram Man page
Histogram,DEGs-method Man page
identity.matrix Man page
identity.matrix,GOsims-method Man page
IdentityPlot Man page
IdentityPlot,GOsims-method Man page
label.condition Man page
label.condition,DEGs-method Man page
label.level.DEGs Man page
label.level.DEGs,DEGs-method Man page
label.level.enriched Man page
label.level.enriched,EnrichedSets-method Man page
limma.DEGs Man page
MAplot Man page
MAplot,DEGs-method Man page
newTranslatomeDataset Man page
Radar Man page
Radar,EnrichedSets-method Man page
Radar,GOsets-method Man page
regulatory.elements.counts Man page
regulatory.elements.regulated Man page
RegulatoryEnrichment Man page
RegulatoryEnrichment,DEGs-method Man page
Scatterplot Man page
Scatterplot,DEGs-method Man page
SDplot Man page
SDplot,DEGs-method Man page
show,DEGs-method Man page
show,EnrichedSets-method Man page
show,GOsets-method Man page
show,TranslatomeDataset-method Man page
significance.threshold Man page
significance.threshold,DEGs-method Man page
similarity.matrix Man page
similarity.matrix,GOsims-method Man page
SimilarityPlot Man page
SimilarityPlot,GOsims-method Man page
tRanslatome Man page
translatome.analysis Man page
tRanslatomeData Man page
TranslatomeDataset-class Man page
tRanslatome-package Man page
tRanslatomeSampleData Man page

Files

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.

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