Package: terapadog 1.5.0

Gionmattia Carancini

terapadog: Translational Efficiency Regulation Analysis using the PADOG Method

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.

Authors:Gionmattia Carancini [cre, aut]

terapadog_1.5.0.tar.gz
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terapadog_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
terapadog/json (API)

# Install 'terapadog' in R:

install.packages('terapadog', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gionmattia/terapadog/issues

On BioConductor:terapadog-1.5.0(bioc 3.24)terapadog-1.4.0(bioc 3.23)

riboseq transcriptomics genesetenrichment generegulation reactome software

3.30 score 9 scripts 5 exports 110 dependencies

Last updated from:54d05ead9b. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	209
linux-devel-x86_64	NOTE	485
source / vignettes	OK	356
linux-release-x86_64	NOTE	549
macos-release-arm64	NOTE	291
macos-oldrel-arm64	NOTE	269
windows-devel	NOTE	452
windows-release	NOTE	484
windows-oldrel	NOTE	508
wasm-release	OK	195

Exports:get_FCs id_converter plotDTA prepareTerapadogData terapadog

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 blob bslib cachem cli codetools cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray DESeq2 digest dplyr evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gtable highr hms htmltools htmlwidgets httr httr2 IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly png prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xml2 XVector yaml

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

Rendered fromterapadog_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-03-05
Started: 2024-11-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
This function execute the Differential Translation Analysis on its own using DeltaTE. The output is a dataframe with the FC in mRNA counts, RIBO counts or TE between the conditions in exam.	get_FCs
Convert the human gene identifier (hgnc_symbol or ensembl_gene_id) to entrezgene_id format for the analysis.	id_converter
This function will plot an interactive html plot of the results of get_FCs.R That is to say, a plot of the genes undergoing translational regulation, coloured by RegMode. Genes whose RegMode was Undeterminable or Undetermined are omitted.	plotDTA
Prepare Data by Loading and Validating RNA, RIBO Counts, and Metadata. This function reads RNA and RIBO count files, checks input data validity and merges them into a single numerical matrix (expression.data). It also prepares the metatadata needed by padog (exp_de).	prepareTerapadogData
Performs the main Gene Set Enrichement Analysis, by applying a modified version of the PADOG algorithm to genes undergoing changes in TE.	terapadog