NEWS
PscanR 0.99.0
- Initial Bioconductor submission.
pscan() implements the Pscan method (Zambelli, Pesole and Pavesi, 2009,
doi:10.1093/nar/gkp464): it tests a set of promoter sequences for
transcription factor binding motifs that score higher than in a background
of all promoters of the organism, and reports z-scores, p-values and FDR.- Precomputed backgrounds for the JASPAR 2020, 2022 and 2024 CORE collections,
seven genome assemblies and five promoter windows are retrieved from
ExperimentHub (package PscanRBackgrounds), or directly from their Zenodo
records, with
ps_retrieve_bg() and listed with ps_available_bg().
- Custom backgrounds can be built with
ps_build_bg() and saved and reloaded
with ps_write_bg_to_file() and ps_retrieve_bg_from_file(). Full
backgrounds keep per-promoter hits, so that pscan_full_bg() can test a set
of transcripts without rescanning sequences.
pscan_filtered() restricts an analysis to motifs that pass a first scan.ps_select_promoters() and ps_selection_summary() choose one promoter per
gene from a gene list.- Results are summarised with
ps_results_table() and visualised with
ps_zscore_heatmap(), ps_motif_barplot(), ps_density_plot(),
ps_hitpos_map() and ps_hit_score_plot().
- Motif scanning can run in parallel through BiocParallel; it is serial by
default.