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clover

clover facilitates analysis and visualization of nanopore tRNA sequencing data, including differential expression, base-calling error analysis, and modification co-occurrence networks.

clover is under active development. Caveat emptor.

Installation

You can install the development version of clover from GitHub with:

# install.packages("pak")
pak::pak("rnabioco/clover")

Example

clover reads output from the aa-tRNA-seq-pipeline and stores the results in a SummarizedExperiment.

Annotated tRNA cloverleaf structure showing known modifications, anticodon highlight, and discriminator base.

Features

clover provides a complete toolkit for nanopore tRNA-seq analysis:

  • Differential tRNA abundance — Test for expression changes between conditions using DESeq2, with volcano plots and tabular summaries.
  • Charging analysis — Measure aminoacylation levels per tRNA and compare across conditions, including joint abundance-charging visualizations.
  • Base-calling error profiles — Visualize per-position error rates that reflect RNA modifications, with annotation overlays from MODOMICS.
  • Modification heatmaps — Map error rate differences to Sprinzl coordinates for cross-tRNA comparison of modification signatures.
  • tRNA secondary structure — Render cloverleaf diagrams annotated with modifications, co-occurrence linkages, and custom highlights (shown above).
  • Modification co-occurrence — Compute odds ratios for pairwise modification co-occurrence and visualize as chord diagrams, arc plots, or structure overlays.

See vignette("clover") for a complete walkthrough.

  • aa-tRNA-seq-pipeline is the Snakemake pipeline that generates the data clover analyzes.
  • R2easyR visualizes structure probing signals on RNA secondary structure diagrams.
  • nanoblot facilitates visualization of nanopore sequencing data, including a “virtual gel” plot.