R: Fungal Assignment Pipeline

# Fungal Assignment Pipeline

## Documentation for package ‘ClassifyITS’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

best_hit_taxonomy_assignment | Hierarchical best-hit taxonomy assignment with per-rank fallback rule
check_N | Check proportion of N bases in each sequence.
consensus_taxonomy_assignment | Per-rank consensus filter for taxonomy assignment
easy_assignments | Easy taxonomy assignment for OTUs using BLAST QC output & phylum-specific thresholds.
ensure_cols | Ensure data frame has all required columns (as character)
ITS_assignment | Complete Fungal Assignment Pipeline
load_and_check | Load and check BLAST results and rep-seq FASTA
parse_taxonomy_cutoffs | Parse taxonomy cutoffs file
plot_alignment_hist | Create and return alignment length histogram (ggplot object)
safe_rbind_list | Safely rbinds list of data frames, ensuring columns match
save_taxonomy_graphics | Save taxonomy summary charts and tables to multi-page PDF
trim_alignments | Trim BLAST alignments by minimum length
write_initial_assignments | Create and write the initial assignments table including drops at all steps