Package: tTEscanR
Title: An advanced R-based package to quantify and visualize
        translation efficiency from sequencing data
Version: 0.99.0
Authors@R: 
    person("Ana", "Varas-Sánchez", 
        email = "ana.varas@scilifelab.se", 
        role = c("aut", "cre"),
        comment = c(ORCID = "0009-0006-0187-8968"))
Description: 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.
License: MIT + file LICENSE
Imports: methods, dplyr, Matrix, stats, tibble, rlang, Biostrings,
        magrittr, purrr, tidyr
Encoding: UTF-8
Depends: R (>= 4.5.0)
VignetteBuilder: knitr
URL: https://github.com/avarassanchez/tTEscanR
BugReports: https://github.com/avarassanchez/tTEscanR/issues
Suggests: testthat, withr, mockery, knitr, rmarkdown, BiocStyle,
        stringr, DESeq2, devtools, SummarizedExperiment, matrixStats,
        pheatmap, ggplot2, ggrepel, viridis, dendsort, biomaRt,
        tRNAscanImport, GenomicRanges, ggradar, S4Vectors, Seurat,
        Signac, Rtsne, ggpubr, IRanges, GenomeInfoDb, uwot,
        ComplexHeatmap, patchwork, Rsamtools
Config/testthat/edition: 3
biocViews: Software, Epitranscriptomics, Transcriptomics,
        GeneExpression, GeneRegulation, Sequencing, SingleCell
Roxygen: list(markdown = TRUE, r6 = FALSE)
RoxygenNote: 8.0.0
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-06-29 21:53:18 UTC
RemoteUrl: https://github.com/BiocStaging/tTEscanR
RemoteRef: HEAD
RemoteSha: d5854c30c1f67560bec105b714505983a0dfb35b
NeedsCompilation: no
Packaged: 2026-06-29 23:01:24 UTC; root
Author: Ana Varas-Sánchez [aut, cre] (ORCID:
    <https://orcid.org/0009-0006-0187-8968>)
Maintainer: Ana Varas-Sánchez <ana.varas@scilifelab.se>