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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tRanslatome")
In most cases, you don't need to download the package archive at all.
tRanslatome
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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see tRanslatome.
Comparison between multiple levels of gene expression
Bioconductor version: 3.4
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.
Author: Toma Tebaldi, Erik Dassi, Galena Kostoska
Maintainer: Toma Tebaldi <tebaldi at science.unitn.it>, Erik Dassi <erik.dassi at unitn.it>
Citation (from within R,
enter citation("tRanslatome")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("tRanslatome")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("tRanslatome")
| R Script | tRanslatome | |
| Reference Manual |
Details
| biocViews | Bioinformatics, CellBiology, DifferentialExpression, GO, GeneExpression, GeneRegulation, HighThroughputSequencing, Microarray, MultipleComparisons, QualityControl, Regulation, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (3.5 years) |
| License | GPL-3 |
| Depends | R (>= 2.15.0), methods, limma, sigPathway, samr, anota, DESeq, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
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| Depends On Me | |
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| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | tRanslatome_1.12.0.tar.gz |
| Windows Binary | tRanslatome_1.12.0.zip |
| Mac OS X 10.9 (Mavericks) | tRanslatome_1.12.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/tRanslatome/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/tRanslatome/ |
| Package Downloads Report | Download Stats |
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