terapadog

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see terapadog.

Translational Efficiency Regulation Analysis using the PADOG Method

Bioconductor version: 3.21

This package performs a Gene Set Analysis with the approach adopted by PADOG on the genes that are reported as translationally regulated (ie. exhibit a significant change in TE) by the DeltaTE package. It can be used on its own to see the impact of translation regulation on gene sets, but it is also integrated as an additional analysis method within ReactomeGSA, where results are further contextualised in terms of pathways and directionality of the change.

Author: Gionmattia Carancini [cre, aut] ORCID iD ORCID: 0000-0001-7936-4883

Maintainer: Gionmattia Carancini <gionmattia at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("terapadog")

terapadog: Translational Efficiency Regulation Analysis & Pathway Analysis with Down-weighting of Overlapping Genes HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneRegulation, GeneSetEnrichment, Reactome, RiboSeq, Software, Transcriptomics

Version 1.0.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License GPL-2

Depends

Imports DESeq2, KEGGREST, stats, utils, dplyr, plotly, htmlwidgets, biomaRt, methods

System Requirements

URL https://github.com/Gionmattia/terapadog

Bug Reports https://github.com/Gionmattia/terapadog/issues

Suggests apeglm, BiocStyle, knitr, rmarkdown, testthat

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Package Archives

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

Source Package terapadog_1.0.0.tar.gz

Windows Binary (x86_64) terapadog_1.0.0.zip (64-bit only)

macOS Binary (x86_64) terapadog_1.0.0.tgz

macOS Binary (arm64) terapadog_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/terapadog

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/terapadog

Bioc Package Browser https://code.bioconductor.org/browse/terapadog/

Package Short Url https://bioconductor.org/packages/terapadog/

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