Package index • clover

Read

read_bcerror(): Read base-calling error ("bcerror") TSV files.
read_charging(): Read a charging CPM file.
read_charging_multi(): Read charging CPM files for multiple samples.
read_counts(): Read a counts TSV file.
read_fasta(): Read FASTA reference
read_mod_annotations(): Read modifications file
read_odds_ratios(): Read an odds ratios file.
read_odds_ratios_multi(): Read odds ratio files for multiple samples.
read_pipeline_config(): Read a Snakemake pipeline configuration file.
read_pipeline_results(): Read pipeline results for all samples.
read_sprinzl_coords(): Read Sprinzl coordinates from a global coordinates TSV file.

abundance_count_matrix(): Build a tRNA abundance count matrix from charging data.
aggregate_or_isodecoder(): Aggregate odds ratios to isodecoder level.
build_coldata(): Build column metadata for DESeq2.
calculate_rewiring_scores(): Calculate rewiring scores from a ROR matrix.
charging_count_matrix(): Build a charging count matrix for differential charging analysis.
clean_odds_ratios(): Clean odds ratio data.
compute_bcerror_delta(): Compute per-position delta between two conditions.
compute_charging_diffs(): Compute charging ratio differences between conditions.
filter_linkages(): Filter odds ratios for structure linkage arcs.
compute_odds_ratios(): Compute pairwise modification co-occurrence odds ratios.
compute_ror(): Compute ratio of odds ratios between conditions.
compute_ror_isodecoder(): Compute relative odds ratio at isodecoder level.
perform_pcoa(): Perform PCoA on a rewiring matrix.
prepare_rewiring_matrix(): Prepare a matrix for rewiring PCoA analysis.
run_deseq(): Run DESeq2 differential analysis.
tabulate_deseq(): Tabulate top DESeq2 differential expression results.
tidy_deseq_results(): Tidy DESeq2 results into a tibble.

prep_mod_heatmap(): Prepare data for plot_mod_heatmap().
plot_abundance_charging(): Plot abundance changes versus charging ratio changes.
plot_arc_diagram(): Plot a network as an arc diagram.
plot_bcerror_profile(): Plot per-position base-calling error profiles.
plot_charging_diffs(): Plot per-tRNA charging ratio differences.
plot_chord_or(): Plot a chord diagram of modification co-occurrence.
plot_chord_ror(): Plot a chord diagram of modification rewiring between conditions.
plot_identity_panel(): Plot identity elements for multiple tRNAs side by side
plot_identity_structure(): Plot tRNA structure with identity element overlays
plot_mod_heatmap(): Plot a delta-signal modification heatmap.
plot_mod_landscape(): Plot per-tRNA modification landscape profiles.
plot_pcoa_rewiring(): Plot PCoA of tRNA rewiring scores.
plot_tRNA_structure(): Plot tRNA secondary structure with modifications and linkages
plot_volcano(): Plot a volcano plot of differential expression results.

default_mod_palette(): Default modification color palette
plot_tRNA_structure(): Plot tRNA secondary structure with modifications and linkages
structure_html(): Embed a tRNA structure SVG as centered HTML
structure_organisms(): List organisms with bundled tRNA structure SVGs
structure_to_png(): Convert a tRNA structure SVG to PNG
structure_trnas(): List available tRNA structures for an organism

modomics_mods(): Map cached MODOMICS modifications onto reference sequences
modomics_organisms(): List organisms with cached MODOMICS data
fetch_modomics_mods(): Fetch tRNA modification annotations from MODOMICS

identity_elements(): Retrieve tRNA aminoacylation identity elements
identity_organisms(): List supported organisms for identity elements
map_identity_to_trna(): Map identity elements to tRNA sequence positions
plot_identity_panel(): Plot identity elements for multiple tRNAs side by side
plot_identity_structure(): Plot tRNA structure with identity element overlays