terapadog
This is the development version of terapadog; to use it, please install the devel version of Bioconductor.
Translational Efficiency Regulation Analysis using the PADOG Method
Bioconductor version: Development (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:
Maintainer: Gionmattia Carancini <gionmattia at gmail.com>
citation("terapadog")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | GeneRegulation, GeneSetEnrichment, Reactome, RiboSeq, Software, Transcriptomics |
| Version | 0.99.6 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| 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 |
See More
| Suggests | apeglm, BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | terapadog_0.99.6.tar.gz |
| Windows Binary (x86_64) | terapadog_0.99.6.zip |
| macOS Binary (x86_64) | terapadog_0.99.6.tgz |
| macOS Binary (arm64) | terapadog_0.99.6.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/ |
| Package Downloads Report | Download Stats |