Overview | Workflow | 1. Loading the data | 2. Setup the tTEscanR object | 2.1 Pre-processing | 2.2. Defining the tTEscanR object | 3. Standard workflow | 3.1. Codon usage assessment | 3.2. Anticodon usage assessment | 3.3. Amio acid level assessment | 3.4. Theoretical Translation Efficiency (tTE) computation | 4. Differential expression analysis | 5. References
Package: tTEscanR 0.99.0
Ana Varas-Sánchez
tTEscanR: An advanced R-based package to quantify and visualize translation efficiency from sequencing data
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.
Authors:
tTEscanR_0.99.0.tar.gz
tTEscanR_0.99.0.zip(r-4.7)tTEscanR_0.99.0.zip(r-4.6)tTEscanR_0.99.0.zip(r-4.5)
tTEscanR_0.99.0.tgz(r-4.6-any)tTEscanR_0.99.0.tgz(r-4.5-any)
tTEscanR_0.99.0.tar.gz(r-4.7-any)tTEscanR_0.99.0.tar.gz(r-4.6-any)
tTEscanR_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tTEscanR/json (API)
| # Install 'tTEscanR' in R: |
| install.packages('tTEscanR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/avarassanchez/ttescanr/issues
Datasets:
- default_tTEscanR_metadata - Metadata of mRNA and tRNA data
- default_tTEscanR_mRNA_data - MRNA Expression Data Subset
- default_tTEscanR_tRNA_data - TRNA Expression Data Subset
softwareepitranscriptomicstranscriptomicsgeneexpressiongeneregulationsequencingsinglecell
Last updated from:d5854c30c1. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 340 | ||
| linux-devel-x86_64 | OK | 1042 | ||
| source / vignettes | OK | 485 | ||
| linux-release-x86_64 | OK | 890 | ||
| macos-release-arm64 | OK | 856 | ||
| macos-oldrel-arm64 | OK | 628 | ||
| windows-devel | OK | 1143 | ||
| windows-release | OK | 1141 | ||
| windows-oldrel | OK | 696 | ||
| wasm-release | OK | 288 |
Exports:computeAAUsagecomputeAnticodonUsagecomputeCodonUsagecomputeCorrelationBackgroundcomputeDEResultscomputeExonicBackgroundcomputeMeanUsagecomputeTheoreticalTEcreateObjectextractCodonsfeaturesToAAgetAssaygetCodonFreqgetMetadatagetPermutationDistgroupConditionsmergeMatricesobtainSignificanceplotCorrelationplotDEResultsplotDistributionplotPermutationplotProportionplotTargetComparisonplotTEscorerunDEAnalysisrunPipelineshowPoolContributiontransformFormattRNAFilterCutstRNAGetMatrixtRNASetCutofftRNASetGenesupdateObject
Dependencies:BiocGenericsBiostringsclicpp11crayondplyrgenericsglueIRangeslatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6rlangS4VectorsSeqinfostringistringrtibbletidyrtidyselectutf8vctrswithrXVector
tTEscanR User Guide
Last update: 2026-06-22
Started: 2025-08-27
tTEscanR tRNA-Specific Preprocessing Module
1. Overview | 2. Obtaining the tRNA matrix | 3. Identifying the optimal tRNA cutoff
Last update: 2026-06-22
Started: 2026-06-12
tTEscanR Codon Frequency-per-Gene Matrix
Overview
Last update: 2026-06-22
Started: 2025-08-27
tTEscanR Visualization Module
1. Overview | 2. Configuration options | 2.1. Data transformation | 2.2. Parameters | 3. Visualization options | 4. References
Last update: 2026-06-22
Started: 2025-08-27
