{ "_id": "6a42fdee4ba05a737d8b467f", "Package": "tTEscanR", "Title": "An advanced R-based package to quantify and visualize\ntranslation efficiency from sequencing data", "Version": "0.99.0", "Authors@R": "person(\"Ana\", \"Varas-Sánchez\",\nemail = \"ana.varas@scilifelab.se\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0006-0187-8968\"))", "Description": "Translation elongation is dependent on codon-anticodon\ninteractions, with suitable nucleotide pairing being essential\nfor efficient translation. To quantify this relationship, we\npreviously developed a computational pipeline (GitHub -\nwgao688/sc_tRNA_mRNA) that uses mRNA codon usage relative to\ntRNA anticodon availability as a proxy for theoretical\ntranslation efficiency (tTE). Here, we introduce tTEscanR, a\npowerful and user-friendly R-based package that extends this\napproach to quantify translation efficiency from both bulk and\nsingle-cell sequencing data. tTEscanR is a versatile tool for\nexploring translation efficiency in diverse cellular processes,\ndisease mechanisms, and therapeutic development. It also\nfeatures an advanced visualization module to generate\nhigh-quality plots, enhancing result interpretation and\ncommunication.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "URL": "https://github.com/avarassanchez/tTEscanR", "BugReports": "https://github.com/avarassanchez/tTEscanR/issues", "Config/testthat/edition": "3", "biocViews": "Software, Epitranscriptomics, Transcriptomics,\nGeneExpression, 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": { "Date": "2026-06-29 23:01:24 UTC", "User": "root" }, "Author": "Ana Varas-Sánchez [aut, cre] (ORCID:\n)", "Maintainer": "Ana Varas-Sánchez ", "MD5sum": "d1f7a5b06db637f0638d524c82ecdea8", "_user": "biocstaging", "_type": "src", "_file": "tTEscanR_0.99.0.tar.gz", "_fileid": "23c30f328dbc1064123859872d87fdf76ba672b90c0d14eccffbbba0a13b7e4e", "_filesize": 5161753, "_sha256": "23c30f328dbc1064123859872d87fdf76ba672b90c0d14eccffbbba0a13b7e4e", "_created": "2026-06-29T23:01:24.000Z", "_published": "2026-06-29T23:21:18.189Z", "_jobs": [ { "job": 84175850153, "time": 340, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "7966774878" }, { "job": 84175850149, "time": 1042, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7966941647" }, { "job": 84175850173, "time": 890, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "7966906332" }, { "job": 84175850158, "time": 628, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7966844655" }, { "job": 84175850148, "time": 856, "config": 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"avarassanchez <84199202+avarassanchez@users.noreply.github.com>", "committer": "GitHub ", "message": "Document AI tools used in package development\n\nAdded a section on AI tools used during development.", "time": 1782769998 }, "_maintainer": { "name": "Ana Varas-Sánchez", "email": "ana.varas@scilifelab.se", "login": "avarassanchez", "description": "", "uuid": 84199202 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { 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"Placenta-AFP_ALB positive cells", "Placenta-Extravillous trophoblasts", "Placenta-IGFBP1_DKK1 positive cells", "Placenta-Lymphoid cells", "Placenta-Megakaryocytes", "Placenta-Myeloid cells", "Placenta-PAEP_MECOM positive cells", "Placenta-Smooth muscle cells", "Placenta-Stromal cells", "Placenta-Syncytiotrophoblasts and villous cytotrophoblasts", "Placenta-Trophoblast giant cells", "Placenta-Vascular endothelial cells", "Lung-Bronchiolar and alveolar epithelial cells", "Lung-Ciliated epithelial cells", "Lung-CSH1_CSH2 positive cells", "Lung-Lymphatic endothelial cells", "Lung-Lymphoid cells", "Lung-Megakaryocytes", "Lung-Mesothelial cells", "Lung-Myeloid cells", "Lung-Neuroendocrine cells", "Lung-Squamous epithelial cells", "Lung-Stromal cells", "Lung-Vascular endothelial cells", "Lung-Visceral neurons", "Spleen-AFP_ALB positive cells", "Spleen-Erythroblasts", "Spleen-Lymphoid cells", "Spleen-Megakaryocytes", "Spleen-Mesothelial cells", "Spleen-Myeloid cells", "Spleen-STC2_TLX1 positive cells", "Spleen-Stromal cells", "Spleen-Vascular endothelial cells", "Eye-Amacrine cells", "Eye-Astrocytes", "Eye-Bipolar cells", "Eye-Corneal and conjunctival epithelial cells", "Eye-Ganglion cells", "Eye-Horizontal cells", "Eye-Lens fibre cells", "Eye-Microglia", "Eye-PDE11A_FAM19A2 positive cells", "Eye-Photoreceptor cells", "Eye-Retinal pigment cells", "Eye-Retinal progenitors and Muller glia", "Eye-Skeletal muscle cells", "Eye-Smooth muscle cells", "Eye-Stromal cells", "Eye-Vascular endothelial cells", "Stomach-Ciliated epithelial cells", "Stomach-ENS glia", "Stomach-ENS neurons", "Stomach-Erythroblasts", "Stomach-Goblet cells", "Stomach-Lymphatic endothelial cells", "Stomach-Lymphoid cells", "Stomach-Mesothelial cells", "Stomach-MUC13_DMBT1 positive cells", "Stomach-Myeloid cells", "Stomach-Neuroendocrine cells", "Stomach-Parietal and chief cells", "Stomach-PDE1C_ACSM3 positive cells", "Stomach-Squamous epithelial cells", "Stomach-Stromal cells", "Stomach-Vascular endothelial cells", "Heart-Cardiomyocytes", "Heart-CLC_IL5RA positive cells", "Heart-ELF3_AGBL2 positive cells", "Heart-Endocardial cells", "Heart-Epicardial fat cells", "Heart-Erythroblasts", "Heart-Lymphatic endothelial cells", "Heart-Lymphoid cells", "Heart-Megakaryocytes", "Heart-Myeloid cells", "Heart-SATB2_LRRC7 positive cells", "Heart-Schwann cells", "Heart-Smooth muscle cells", "Heart-Stromal cells", "Heart-Vascular endothelial cells", "Heart-Visceral neurons", "Thymus-Antigen presenting cells", "Thymus-Stromal cells", "Thymus-Thymic epithelial cells", "Thymus-Thymocytes", "Thymus-Vascular endothelial cells", "Intestine-Chromaffin cells", "Intestine-ENS glia", "Intestine-ENS neurons", "Intestine-Erythroblasts", "Intestine-Intestinal epithelial cells", "Intestine-Lymphatic endothelial cells", "Intestine-Lymphoid cells", "Intestine-Mesothelial cells", "Intestine-Myeloid cells", "Intestine-Smooth muscle cells", "Intestine-Stromal cells", "Intestine-Vascular endothelial cells" ], 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"table": true, "tojson": true } ], "_help": [ { "page": "ComputeAAUsage", "title": "Compute Amino Acid (AA) Demand or Supply", "topics": [ "computeAAUsage" ] }, { "page": "ComputeAnticodonUsage", "title": "Compute Anticodon Usage from tRNA Gene Expression Data", "topics": [ "computeAnticodonUsage" ] }, { "page": "ComputeCodonUsage", "title": "Compute Codon Usage from mRNA Gene Expression Data", "topics": [ "computeCodonUsage" ] }, { "page": "ComputeCorrelationBackground", "title": "Compute the Correlation Between Mean Usage and Exonic Background", "topics": [ "computeCorrelationBackground" ] }, { "page": "ComputeDEResults", "title": "Compute the DESeq2 Analysis", "topics": [ "computeDEResults" ] }, { "page": "ComputeExonicBackground", "title": "Compute the Exonic Background of the Codon/Anticodon Usage", "topics": [ "computeExonicBackground" ] }, { "page": "ComputeMeanUsage", "title": "Compute Usage Across Conditions (Mean Usage)", "topics": [ "computeMeanUsage" ] }, { "page": "computeTheoreticalTE", "title": "Compute the Theoretical Translation Efficiency (tTE) score", "topics": [ "computeTheoreticalTE" ] }, { "page": "CreateObject", "title": "Create a tTEscanR Object", "topics": [ "createObject" ] }, { "page": "default_tTEscanR_metadata", "title": "Metadata of mRNA and tRNA data", "topics": [ "default_tTEscanR_metadata" ] }, { "page": "default_tTEscanR_mRNA_data", "title": "mRNA Expression Data Subset", "topics": [ "default_tTEscanR_mRNA_data" ] }, { "page": "default_tTEscanR_tRNA_data", "title": "tRNA Expression Data Subset", "topics": [ "default_tTEscanR_tRNA_data" ] }, { "page": "ExtractCodons", "title": "Extract Codon Composition of Sequences", "topics": [ "extractCodons" ] }, { "page": "FeaturesToAA", "title": "Relates Codons, Anticodons and their corresponding Amino Acids", "topics": [ "featuresToAA" ] }, { "page": "getAssay", "title": "Get Assay Data from a tTEscanR Object", "topics": [ "getAssay", "getAssay,tTEscanR_Object-method" ] }, { "page": "GetCodonFreq", "title": "Compute Codon Frequency-per-Gene Table", "topics": [ "getCodonFreq" ] }, { "page": "getMetadata", "title": "Get Metadata from a tTEscanR Object", "topics": [ "getMetadata", "getMetadata,tTEscanR_Object-method" ] }, { "page": "GetPermutationDist", "title": "Run Codon Usage Permutation Test (Background)", "topics": [ "getPermutationDist" ] }, { "page": "GroupConditions", "title": "Aggregates data by group", "topics": [ "groupConditions" ] }, { "page": "MergeMatrices", "title": "Combine large matrices", "topics": [ "mergeMatrices" ] }, { "page": "ObtainSignificance", "title": "Assess Significance (P-value) & Corrects for Multiple Hypothesis Testing", "topics": [ "obtainSignificance" ] }, { "page": "PlotCorrelation", "title": "Correlation Plot: Exonic Codon Background - Mean Codon Usage", "topics": [ "plotCorrelation" ] }, { "page": "PlotDEResults", "title": "Generates Visualizations from the DEA data", "topics": [ "plotDEResults" ] }, { "page": "PlotDistribution", "title": "Distribution Plot of Codon/Anticodon Usage or Amino Acid Demand/Supply", "topics": [ "plotDistribution" ] }, { "page": "PlotPermutation", "title": "Permutation Plot", "topics": [ "plotPermutation" ] }, { "page": "PlotProportion", "title": "Proportion Plot of Codon/Anticodon Usage or Amino Acid Demand/Supply", "topics": [ "plotProportion" ] }, { "page": "PlotTargetComparison", "title": "Distribution Plot of Codon/Anticodon Usage or Amino Acid Demand/Supply Compared to a Target", "topics": [ "plotTargetComparison" ] }, { "page": "PlotTEscore", "title": "Violin Plot Displaying tTE Scores", "topics": [ "plotTEscore" ] }, { "page": "RunDEAnalysis", "title": "Perform Differential Expression Analysis Using DESeq2", "topics": [ "runDEAnalysis" ] }, { "page": "RunPipeline", "title": "Runs the Theoretical Translation Efficiency (tTE) Pipeline", "topics": [ "runPipeline" ] }, { "page": "ShowPoolContribution", "title": "Examine the Codon Pool Contribution", "topics": 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