Package: tRanslatome 1.51.0

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:Toma Tebaldi, Erik Dassi, Galena Kostoska

tRanslatome_1.51.0.tar.gz
tRanslatome_1.51.0.zip(r-4.7)tRanslatome_1.51.0.zip(r-4.6)tRanslatome_1.51.0.zip(r-4.5)
tRanslatome_1.51.0.tgz(r-4.6-any)tRanslatome_1.51.0.tgz(r-4.5-any)
tRanslatome_1.51.0.tar.gz(r-4.7-any)tRanslatome_1.51.0.tar.gz(r-4.6-any)
tRanslatome_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tRanslatome/json (API)

# Install 'tRanslatome' in R:

install.packages('tRanslatome', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

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-1.51.0(bioc 3.24)tRanslatome-1.50.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cellbiology generegulation regulation geneexpression differentialexpression microarray highthroughputsequencing qualitycontrol go multiplecomparisons bioinformatics

3.30 score 3 scripts 1 mentions 34 exports 100 dependencies

Last updated from:16e40951f6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	231
linux-devel-x86_64	NOTE	411
source / vignettes	OK	392
linux-release-x86_64	NOTE	445
macos-release-arm64	NOTE	217
macos-oldrel-arm64	NOTE	217
windows-devel	NOTE	350
windows-release	NOTE	332
windows-oldrel	NOTE	331
wasm-release	OK	217

Exports:average.similarity.scores computeDEGs CVplot DEGs.table enriched.table FC.threshold getConditionA getConditionB getConditionC getConditionD getConditionLabels getDataType getDEGs getDEGsMethod getExprMatrix getLevelLabels GOComparison GOEnrichment Heatmap Histogram identity.matrix IdentityPlot label.condition label.level.DEGs label.level.enriched MAplot newTranslatomeDataset Radar RegulatoryEnrichment Scatterplot SDplot significance.threshold similarity.matrix SimilarityPlot

Dependencies:abind AnnotationDbi anota askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob cachem caTools cli codetools cpp11 crayon curl DBI DelayedArray DESeq2 digest edgeR farver fastmap formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gmp GO.db GOSemSim gplots graph gtable gtools Heatplus httr IRanges isoband jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime multtest openssl org.Hs.eg.db pkgconfig plotrix plyr png qvalue R6 RankProd rappdirs RColorBrewer Rcpp RcppArmadillo reshape2 rlang Rmpfr RSQLite S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys topGO vctrs viridisLite withr XVector yulab.utils

tRanslatome

Rendered fromtRanslatome_package.Rnwusingutils::Sweave

Last update: 2018-08-03
Started: 2013-06-05

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

Package: tRanslatome 1.51.0

tRanslatome: Comparison between multiple levels of gene expression

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