tTEscanR
This is the development version of tTEscanR; to use it, please install the devel version of Bioconductor.
A user-friendly integrative R package for quantifying and visualizing translation efficiency from sequencing data in diverse biological systems
Bioconductor version: Development (3.24)
Translation elongation is dependent on codon-anticodon interactions, with suitable nucleotide pairing being essential for efficient translation. To quantify this relationship, we previously developed a computational pipeline (GitHub - wgao688/sc_tRNA_mRNA) that uses mRNA codon usage relative to tRNA anticodon availability as a proxy for theoretical translation efficiency (tTE). Here, we introduce tTEscanR, a powerful and user-friendly R-based package that extends this approach to quantify translation efficiency from both bulk and single-cell sequencing data. tTEscanR is a versatile tool for exploring translation efficiency in diverse cellular processes, disease mechanisms, and therapeutic development. It also features an advanced visualization module to generate high-quality plots, enhancing result interpretation and communication.
Author: Ana Varas-Sánchez [aut, cre] 
, Carlos Gallardo-Dodd [aut] , William Gao [aut] , Claudia Kutter [ths] , Karolinska Institutet [fnd] (grant_id: KID-2021-00308, KID-2023-01298), Swedish Research Council [fnd] (grant_id: 2023-02780), Cancerfonden [fnd] (grant_id: 22 2246 Pj, 25 4703 Pj)
Maintainer: Ana Varas-Sánchez <ana.varas at scilifelab.se>
citation("tTEscanR")):Ana Varas-Sánchez, Carlos Gallardo-Dodd, William Gao. tTEscanR: A user-friendly integrative R package for quantifying and visualizing translation efficiency from sequencing data in diverse biological systems. doi:10.18129/B9.bioc.tTEscanR, R package version 0.99.2, https://bioconductor.org/packages/tTEscanR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("tTEscanR")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("tTEscanR")| tTEscanR Codon Frequency-per-Gene Matrix | HTML |
| tTEscanR tRNA-Specific Preprocessing Module | HTML |
| tTEscanR User Guide | HTML |
| tTEscanR Visualization Module | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | CellBasedAssays, Epitranscriptomics, GeneExpression, GeneRegulation, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | stats, SummarizedExperiment, Biostrings, S4Vectors, MultiAssayExperiment, Matrix, DESeq2, matrixStats, tibble, dplyr, tRNAscanImport, GenomicRanges, Signac, utils, biomaRt, stringr, ggplot2, ggrepel, uwot, Rtsne, dendsort, grid, ComplexHeatmap, viridis, tidyr, ggpubr, patchwork, purrr, magrittr, rlang |
| System Requirements | |
| URL | https://github.com/avarassanchez/tTEscanR |
| Bug Reports | https://github.com/avarassanchez/tTEscanR/issues |
See More
| Suggests | testthat, withr, mockery, knitr, rmarkdown, BiocStyle, devtools, pheatmap, Seurat, IRanges, GenomeInfoDb, Rsamtools |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/tTEscanR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tTEscanR |
| Package Short Url | https://bioconductor.org/packages/tTEscanR/ |
| Package Downloads Report | Download Stats |