Package index • floundeR

Run-Level QC Contracts

Tidy sequencing-summary QC tables and report-card checks.

qc_run_summary(): Summarise a nanopore run for QC handoff
qc_yield_over_time() qc_read_length_distribution() qc_quality_distribution() qc_channel_density() qc_barcode_composition(): Build tidy QC data from sequencing-summary inputs
qc_report_card_thresholds() qc_report_card(): Build a run-level QC report card

Rust-backed POD5 discovery, integrity, manifest, and selected ONT Zymo open-data helpers.

pod5_compare(): Compare two POD5 collections or manifests
pod5_file_info(): Inspect local POD5 file metadata
pod5_find(): Discover local POD5-containing folders
pod5_folder_info(): Summarise a local POD5 folder or run tree
pod5_manifest(): Build a versioned POD5 collection manifest
pod5_subdivide_plan(): Plan a read-only POD5 collection subdivision
pod5_verify(): Verify a local POD5 candidate file
ont_open_data_fetch(): Fetch one ONT open-data object into an explicit cache directory
ont_open_data_list() flounder_ont_zymo_pod5_prefix(): List objects in an ONT open-data S3 prefix
ont_zymo_pod5_dataset(): Describe the canonical ONT Zymo fecal POD5 dataset
ont_zymo_pod5_example_objects(): Return selected ONT Zymo fecal POD5 example objects

Curated alignment-level QC wrappers backed by Bamana semantics.

Curated Porkchop-backed kit, adapter, primer, barcode, and cDNA QC evidence.

library_kit_candidates() library_adapter_primer_evidence() library_barcode_evidence() library_cdna_primer_evidence(): Porkchop library-preparation QC evidence
library_preparation_report_card(): Build a library-preparation QC report card
library_preparation_report_card_thresholds(): Default library-preparation report-card thresholds

Versioned JSON payloads for Mnemosyne/Synoptikon QC review.

as_synoptikon_qc() write_synoptikon_qc(): Build and write Synoptikon QC payloads

Semantic report elements, figure handoff, controlled R plot rendering, runtime discovery, and Mnemosyne theme descriptors.

grammateus_figure_from_file() grammateus_figure_from_ggplot(): Build Grammateus figure metadata from image artifacts
grammateus_mnemosyne_theme() grammateus_apply_theme(): Build Mnemosyne Grammateus report theme metadata
grammateus_plot_spec() grammateus_render_plot(): Build and render Grammateus semantic plot specifications
grammateus_render_element() grammateus_render_figure_html() grammateus_render_figure_pdf(): Render Grammateus report elements through the Rust binding
grammateus_report_element() grammateus_qc_report_elements(): Build Grammateus semantic report elements
grammateus_runtime_available() grammateus_runtime_version() grammateus_runtime_manifest() grammateus_runtime_validate() grammateus_runtime_install(): Discover and validate a prebuilt Grammateus runtime
qc_report(): Assemble a Grammateus-backed QC report contract
qc_plot_yield_over_time() qc_plot_quality_distribution() qc_plot_read_length_distribution() qc_plot_flowcell_density() qc_plot_barcode_balance() qc_plot_pod5_integrity() qc_plot_bam_mapping_summary() qc_plot_bam_mapq_distribution() qc_plot_bam_flag_summary(): Build Grammateus plot specs for nanopore QC report families

Helpers for detecting and skipping optional compiled Rust support.

flounder_rust_capabilities() flounder_rust_available() skip_if_no_flounder_rust(): Query compiled Rust support

File wrappers and helpers retained outside the retired FAST5 API.

Fasta: R6 Class for loading and analysing FASTA files
Fastq: R6 Class for loading and analysing nanopore (and other) FASTQ files
Blast: R6 Class for loading and analysing BLAST results in basic Pairwise format
GenbankGenome: R6 Class for loading and analysing Genbank whole genome files
SequencingSummary: R6 Class for loading and analysing nanopore sequencing_summary files
SequencingSet: R6 Class for loading and analysing sequence sets
Flowcell: R6 Class for performing Flowcell centric analyses
MultiplexSet: R6 Class for loading, visualising and analysing barcode information
TemporalSet: R6 Class for analysing sequence sets with accompanying temporal data
BamFile: R6 class for legacy BAM file references
FloundeR: R6 Class for floundeR based analyses
flnDr(): extract a floundeR packaged file
phredmean(): calculate mean Phred scores from list of Q values
qualToMeanQ(): calculate mean Phred score from an ASCII encoded phred string
to_flowcell(): Prepare a flowcell object from provided class
to_sequencing_set(): Prepare a SequencingSet object from provided class

Legacy graphical classes and themes retained for compatibility.

Angenieux: R6 Class for visualising floundeR based datasets
AngenieuxDecoration: R6 Class for describing additional Angenieux decorations
Infographic: R6 Class for loading and analysing sequence sets
InfographicItem: R6 Class for loading and analysing sequence sets