Last data update: 2014.03.03
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tRanslatome
Package: tRanslatome
Type: Package
Title: Comparison between multiple levels of gene expression
Version: 1.10.0
Date: 2015-08-20
Author: Toma Tebaldi, Erik Dassi, Galena Kostoska
Maintainer: Toma Tebaldi <tebaldi@science.unitn.it>, Erik Dassi <erik.dassi@unitn.it>
Depends: R (>= 2.15.0), methods, limma, sigPathway, samr, anota, DESeq,
edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus,
gplots, plotrix, Biobase
Description: 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.
License: GPL-3
LazyLoad: yes
biocViews: CellBiology, GeneRegulation, Regulation, GeneExpression,
DifferentialExpression, Microarray, HighThroughputSequencing,
QualityControl, GO, MultipleComparisons, Bioinformatics
Packaged: 2016-05-04 04:58:42 UTC; biocbuild
NeedsCompilation: no
● BiocViews: Bioinformatics, CellBiology, DifferentialExpression, GO, GeneExpression, GeneRegulation, HighThroughputSequencing, Microarray, MultipleComparisons, QualityControl, Regulation
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8 images,
40 functions,
1 datasets
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Reverse Depends: 0
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'tRanslatome' ...
** R
** data
** inst
** preparing package for lazy loading
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
converting help for package 'tRanslatome'
finding HTML links ... done
CVplot html
DEGs html
DEGs.table html
EnrichedSets html
FC.threshold html
GOComparison html
GOEnrichment html
GOsets html
GOsims html
Heatmap html
Histogram html
IdentityPlot html
MAplot html
Radar html
RegulatoryEnrichment html
SDplot html
Scatterplot html
SimilarityPlot html
TranslatomeDataset html
average.similarity.scores html
computeDEGs html
enriched.table html
getConditionA html
getConditionB html
getConditionC html
getConditionD html
getConditionLabels html
getDEGs html
getDEGsMethod html
getDataType html
getExprMatrix html
getLevelLabels html
identity.matrix html
label.condition html
label.level.DEGs html
label.level.enriched html
newTranslatomeDataset html
significance.threshold html
similarity.matrix html
tRanslatome-package html
tRanslatomeSampleData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (tRanslatome)
Making 'packages.html' ... done
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