Changelog

Source: NEWS.md

tidypq (development version)

• chimera_removal_vs_ref() removes chimeric sequences using UCHIME reference-based detection via vsearch.
• contam_blocklist_pq() flags taxa whose genus belongs to a curated blocklist of known reagent and laboratory contaminants (compiled from Salter et al. 2014, micRoclean and GRIMER), a taxonomy-only method requiring no negative controls; the accompanying known_contaminant_genera() returns the default blocklist for inspection or extension.
• contam_corr_pq() detects potential contaminant taxa by examining the correlation between each taxon’s relative abundance and total sample reads. Contaminants show a negative correlation (higher proportion in low-biomass samples). Returns per-taxon statistics (cor_abs, cor_rel, slope, p_value), a flagged contaminants subset, and a three-panel diagnostic plot. Inspired by the GRIMER tool.
• neg_control_classify_pq() classifies taxa found in negative controls into artifact, lab_contaminant and sample_contaminant categories based on read abundance and occurrence patterns, returning the per-taxon classification together with summary, distribution, heatmap and ordination plots.

tidypq 0.1.0

• Initial CRAN submission.
• filter_samples_pq(), select_samdata_pq(), mutate_samdata_pq(), slice_samples_pq(), arrange_samples_pq(), and rename_samples_pq() provide tidyverse-style verbs for manipulating sample data in ‘phyloseq’ objects.
• filter_taxa_pq(), select_taxa_pq(), mutate_taxa_pq(), slice_taxa_pq(), arrange_taxa_pq(), and rename_taxa_pq() provide tidyverse-style verbs for manipulating taxonomy data.
• filter_occurrences_pq() and mutate_occurrences_pq() allow cell-level operations on the OTU table with special variables (sample_total, taxon_total, etc.).
• filter_tree_pq() filters phylogenetic trees by taxa names or tip label patterns.
• taxa_prevalence() computes per-taxon prevalence across samples.
• decontam_sam_control() and decontam_taxa_control() remove contaminants using negative controls or control taxa.
• chimera_removal_dada2() removes chimeric sequences using ‘dada2’.
• create_chimera_pq() generates synthetic chimeric sequences for benchmarking chimera detection.