tRanslatome
Comparison between multiple levels of gene expression
Bioconductor version: 3.24 · Package version: 1.51.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tRanslatome")Details
| Maintainer | Toma Tebaldi <toma.tebaldi@unitn.it>, Erik Dassi <erik.dassi@unitn.it> |
| Author | Toma Tebaldi, Erik Dassi, Galena Kostoska |
| License | GPL-3 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bioinformatics, CellBiology, DifferentialExpression, GO, GeneExpression, GeneRegulation, HighThroughputSequencing, Microarray, MultipleComparisons, QualityControl, Regulation, Software |
| Package Short Url | https://bioconductor.org/packages/tRanslatome/ |
Citation
From within R, enter citation("tRanslatome"):
Toma Tebaldi, Erik Dassi, Galena Kostoska. tRanslatome: Comparison between multiple levels of gene expression. doi:10.18129/B9.bioc.tRanslatome, R package version 1.51.0, https://bioconductor.org/packages/tRanslatome.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | tRanslatome_1.51.0.tar.gz |
| Windows binary (x86_64) | tRanslatome_1.51.0.zip |
| macOS binary (arm64) | tRanslatome_1.51.0.tgz |
| macOS binary (x86_64) | tRanslatome_1.51.0.tgz |