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returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","rna-seq","trna-annotation"],"created_at":"2026-04-03T03:04:13.438Z","updated_at":"2026-04-03T03:04:18.196Z","avatar_url":"https://github.com/rnabioco.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n```{r}\n#| include: false\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# clover\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/rnabioco/clover/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rnabioco/clover/actions/workflows/R-CMD-check.yaml)\n\u003c!-- badges: end --\u003e\n\nclover facilitates analysis and visualization of nanopore tRNA sequencing\ndata, including differential expression, base-calling error analysis, and\nmodification co-occurrence networks.\n\n**clover is under active development.** *Caveat emptor*.\n\n## Installation\n\nYou can install the development version of clover from\n[GitHub](https://github.com/rnabioco/clover) with:\n\n``` r\n# install.packages(\"pak\")\npak::pak(\"rnabioco/clover\")\n```\n\n## Features\n\nclover provides a complete toolkit for nanopore tRNA-seq analysis:\n\n- **Differential tRNA abundance** --- Test for expression changes between conditions using DESeq2, with volcano plots and tabular summaries.\n- **Charging analysis** --- Measure aminoacylation levels per tRNA and compare across conditions, including joint abundance-charging visualizations.\n- **Base-calling error profiles** --- Visualize per-position error rates that reflect RNA modifications, with annotation overlays from [MODOMICS](https://genesilico.pl/modomics/).\n- **Modification heatmaps** --- Map error rate differences to Sprinzl coordinates for cross-tRNA comparison of modification signatures.\n- **tRNA secondary structure** --- Render cloverleaf diagrams annotated with modifications, co-occurrence linkages, and custom highlights (shown above).\n- **Modification co-occurrence** --- Compute odds ratios for pairwise modification co-occurrence and visualize as chord diagrams, arc plots, or structure overlays.\n\nclover is very opinionated about file inputs and assumes that data have been processed by the [aa-tRNA-seq-pipeline](https://github.com/rnabioco/aa-tRNA-seq-pipeline).\n\n## Example\n\nclover ships tRNA structure references for major expeirmental systems that enable\nstructure-based tRNA annotation.\n\n```{r}\n#| label: example\n#| echo: false\n#| warning: false\n#| message: false\n#| results: hide\nlibrary(clover)\nlibrary(dplyr)\n\ntrna_fasta \u003c- clover_example(\"ecoli/trna_only.fa.gz\")\nmods \u003c- modomics_mods(trna_fasta, organism = \"Escherichia coli\")\n\nmods_glu \u003c- mods |\u003e\n  filter(ref == \"host-tRNA-Glu-TTC-1-1\")\n\n# Look up sequence positions for Sprinzl anticodon (34-36) and\n# discriminator base (73)\nsprinzl \u003c- read_sprinzl_coords(\n  clover_example(\"sprinzl/ecoliK12_global_coords.tsv.gz\")\n)\nglu_coords \u003c- sprinzl |\u003e\n  filter(trna_id == \"tRNA-Glu-UUC-1-1\")\n\nac_pos \u003c- glu_coords |\u003e\n  filter(sprinzl_label %in% c(\"34\", \"35\", \"36\")) |\u003e\n  pull(pos)\n\ndisc_pos \u003c- glu_coords |\u003e\n  filter(sprinzl_label == \"73\") |\u003e\n  pull(pos)\n\nanticodon \u003c- tibble::tibble(\n  pos = ac_pos,\n  mod1 = rep(\"anticodon\", 3)\n)\n\nall_mods \u003c- bind_rows(mods_glu, anticodon)\ndisc_outline \u003c- tibble::tibble(pos = disc_pos, group = \"discriminator\")\ndisc_text \u003c- tibble::tibble(pos = disc_pos, color = \"#E41A1C\")\n\nsvg_path \u003c- plot_tRNA_structure(\n  \"tRNA-Glu-TTC\",\n  \"Escherichia coli\",\n  modifications = all_mods,\n  mod_palette = c(default_mod_palette(), anticodon = \"#4DAF4A\"),\n  outlines = disc_outline,\n  outline_palette = c(discriminator = \"#E41A1C\"),\n  text_colors = disc_text\n)\n\ndest \u003c- \"man/figures/README-structure-annotated.svg\"\nfile.copy(svg_path, dest, overwrite = TRUE)\n```\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"man/figures/README-structure-annotated.svg\" width=\"350\" alt=\"Annotated tRNA cloverleaf structure showing known modifications, anticodon highlight, and discriminator base.\"\u003e\n\u003c/p\u003e\n\nSee `vignette(\"clover\")` for a complete walkthrough.\n\n## Related work\n\n- [aa-tRNA-seq-pipeline](https://github.com/rnabioco/aa-tRNA-seq-pipeline) is the Snakemake pipeline that generates the data clover analyzes.\n- [R2easyR](https://github.com/JPSieg/R2easyR) visualizes structure probing signals on RNA secondary structure diagrams.\n- [nanoblot](https://github.com/SamDeMario-lab/NanoBlot) facilitates visualization of nanopore sequencing data, including a \"virtual gel\" plot.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnabioco%2Fclover","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frnabioco%2Fclover","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnabioco%2Fclover/lists"}