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tRanslatome

Comparison between multiple levels of gene expression


Bioconductor version: Release (3.18)

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.

Author: Toma Tebaldi, Erik Dassi, Galena Kostoska

Maintainer: Toma Tebaldi <toma.tebaldi at unitn.it>, Erik Dassi <erik.dassi at unitn.it>

Citation (from within R, enter citation("tRanslatome")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tRanslatome")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("tRanslatome")
tRanslatome PDF R Script
Reference Manual PDF

Details

biocViews Bioinformatics, CellBiology, DifferentialExpression, GO, GeneExpression, GeneRegulation, HighThroughputSequencing, Microarray, MultipleComparisons, QualityControl, Regulation, Software
Version 1.40.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-3
Depends R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package tRanslatome_1.40.0.tar.gz
Windows Binary tRanslatome_1.40.0.zip (64-bit only)
macOS Binary (x86_64) tRanslatome_1.40.0.tgz
macOS Binary (arm64) tRanslatome_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tRanslatome
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tRanslatome
Bioc Package Browser https://code.bioconductor.org/browse/tRanslatome/
Package Short Url https://bioconductor.org/packages/tRanslatome/
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