Package: tRanslatome 1.45.0
Toma Tebaldi
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, 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.
Authors:
tRanslatome_1.45.0.tar.gz
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tRanslatome_1.45.0.tgz(r-4.4-any)tRanslatome_1.45.0.tgz(r-4.3-any)
tRanslatome_1.45.0.tar.gz(r-4.5-noble)tRanslatome_1.45.0.tar.gz(r-4.4-noble)
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tRanslatome.pdf |tRanslatome.html✨
tRanslatome/json (API)
| # Install 'tRanslatome' in R: |
| install.packages('tRanslatome', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- CCComparison - Sample data set for tRanslatome
- CCEnrichment - Sample data set for tRanslatome
- expressionMatrix - Sample data set for tRanslatome
- limma.DEGs - Sample data set for tRanslatome
- regulatory.elements.counts - Sample data set for tRanslatome
- regulatory.elements.regulated - Sample data set for tRanslatome
- translatome.analysis - Sample data set for tRanslatome
On BioConductor:tRanslatome-1.45.0(bioc 3.21)tRanslatome-1.44.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
cellbiologygeneregulationregulationgeneexpressiondifferentialexpressionmicroarrayhighthroughputsequencingqualitycontrolgomultiplecomparisonsbioinformatics
Last updated 2 months agofrom:7c3a2dc7c8. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 27 2024 |
| R-4.5-win | NOTE | Nov 27 2024 |
| R-4.5-linux | NOTE | Dec 27 2024 |
| R-4.4-win | NOTE | Nov 27 2024 |
| R-4.4-mac | NOTE | Dec 27 2024 |
| R-4.3-win | NOTE | Nov 27 2024 |
| R-4.3-mac | NOTE | Dec 27 2024 |
Exports:average.similarity.scorescomputeDEGsCVplotDEGs.tableenriched.tableFC.thresholdgetConditionAgetConditionBgetConditionCgetConditionDgetConditionLabelsgetDataTypegetDEGsgetDEGsMethodgetExprMatrixgetLevelLabelsGOComparisonGOEnrichmentHeatmapHistogramidentity.matrixIdentityPlotlabel.conditionlabel.level.DEGslabel.level.enrichedMAplotnewTranslatomeDatasetRadarRegulatoryEnrichmentScatterplotSDplotsignificance.thresholdsimilarity.matrixSimilarityPlot
Dependencies:abindAnnotationDbianotaaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemcaToolsclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayDESeq2digestedgeRfansifarverfastmapformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegmpGO.dbGOSemSimgplotsgraphgtablegtoolsHeatplushttrIRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemulttestmunsellnlmeopensslorg.Hs.eg.dbpillarpkgconfigplogrplotrixplyrpngqvalueR.methodsS3R.ooR.utilsR6RankProdRColorBrewerRcppRcppArmadilloreshape2rlangRmpfrRSQLiteS4ArraysS4VectorsscalessnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletopGOUCSC.utilsutf8vctrsviridisLitewithrXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| tRanslatome | tRanslatome-package tRanslatome |
| labelLevelsGOSetsHelpfile | average.similarity.scores |
| computeDEGsHelpfile | computeDEGs |
| CVplotDEGsHelpfile | CVplot |
| Class 'DEGs' | CVplot,DEGs-method DEGs-class DEGs.table,DEGs-method FC.threshold,DEGs-method getDEGsMethod,DEGs-method GOEnrichment,DEGs-method Histogram,DEGs-method label.condition,DEGs-method label.level.DEGs,DEGs-method MAplot,DEGs-method RegulatoryEnrichment,DEGs-method Scatterplot,DEGs-method SDplot,DEGs-method show,DEGs-method significance.threshold,DEGs-method |
| DEGsTableDEGsHelpfile | DEGs.table |
| enrichedtableenrichedSetsHelpfile | enriched.table |
| Class 'EnrichedSets' | enriched.table,EnrichedSets-method EnrichedSets-class Heatmap,EnrichedSets-method label.level.enriched,EnrichedSets-method Radar,EnrichedSets-method show,EnrichedSets-method |
| FCThresholdDEGsHelpfile | FC.threshold |
| getConditionATranslatomeDatasetHelpfile | getConditionA |
| getConditionBTranslatomeDatasetHelpfile | getConditionB |
| getConditionCTranslatomeDatasetHelpfile | getConditionC |
| getConditionDTranslatomeDatasetHelpfile | getConditionD |
| getConditionLabelsTranslatomeDatasetHelpfile | getConditionLabels |
| getDataTypeTranslatomeDatasetHelpfile | getDataType |
| getDEGsTranslatomeDatasetHelpfile | getDEGs |
| getDEGsMethodDEGsHelpfile | getDEGsMethod |
| getExprMatrixTranslatomeDatasetHelpfile | getExprMatrix |
| getLevelLabelsTranslatomeDatasetHelpfile | getLevelLabels |
| GOComparisonHelpfile | GOComparison |
| GOEnrichmentHelpfile | GOEnrichment |
| Class 'GOsets' | GOComparison,GOsets-method GOsets-class Heatmap,GOsets-method Radar,GOsets-method show,GOsets-method |
| Class 'GOsims' | average.similarity.scores,GOsims-method GOsims-class identity.matrix,GOsims-method IdentityPlot,GOsims-method similarity.matrix,GOsims-method SimilarityPlot,GOsims-method |
| HeatmapEnrichedHelpfile | Heatmap |
| HistogramHelpfile | Histogram |
| labelLevelsGOSetsHelpfile | identity.matrix |
| IdentityPlotHelpfile | IdentityPlot |
| labelConditionDEGsHelpfile | label.condition |
| labelLevelDEGsHelpfile | label.level.DEGs |
| labelLevelsEnrichedSetsHelpfile | label.level.enriched |
| MAplotHelpfile | MAplot |
| newTranslatomeDatasetHelpfile | newTranslatomeDataset |
| RadarEnrichedHelpfile | Radar |
| RegulatoryEnrichmentHelpfile | RegulatoryEnrichment |
| ScatterplotHelpfile | Scatterplot |
| SDplotHelpfile | SDplot |
| significanceThresholdDEGsHelpfile | significance.threshold |
| similaritymatrixGOSetsHelpfile | similarity.matrix |
| SimilarityPlotHelpfile | SimilarityPlot |
| Class 'TranslatomeDataset' | computeDEGs,TranslatomeDataset-method getConditionA,TranslatomeDataset-method getConditionB,TranslatomeDataset-method getConditionC,TranslatomeDataset-method getConditionD,TranslatomeDataset-method getConditionLabels,TranslatomeDataset-method getDataType,TranslatomeDataset-method getDEGs,TranslatomeDataset-method getExprMatrix,TranslatomeDataset-method getLevelLabels,TranslatomeDataset-method show,TranslatomeDataset-method TranslatomeDataset-class |
| Sample data set for tRanslatome | CCComparison CCEnrichment expressionMatrix limma.DEGs regulatory.elements.counts regulatory.elements.regulated translatome.analysis tRanslatomeData tRanslatomeSampleData |
