# Downstream analyses of promoter sequence architectures and HTML report generation

## Documentation for package ‘seqArchRplus’ version 1.9.0

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

## Help Pages

curate_clusters | Curate clusters from seqArchR result
form_combined_panel | Form a combined panel of three plots
generate_all_plots | Generate all plots for a given sample
generate_html_report | Generate HTML report with scrollable combined panel plots
handle_tc_from_cage | Handle writing of tag clusters (TCs) from CAGE experiment to disk as BED files.
iqw_tpm_plots | IQW, TPM plots
order_clusters_iqw | Order clusters by median or mean interquantile widths
per_cluster_annotations | per_cluster_annotations
per_cluster_go_term_enrichments | Perform per cluster GO term enrichment analysis
per_cluster_seqlogos | Plot per cluster sequence logos
per_cluster_strand_dist | Visualize as barplots how promoters in each cluster are distributed on different chromosomes and strands
plot_motif_heatmaps | Plot heatmaps of motifs occurring in seqArchR clusters
plot_motif_heatmaps2 | Plot heatmaps of motifs occurring in seqArchR clusters
seqArchRplus | seqArchRplus: A package for downstream analyses of promoter sequence architectures/clusters identified by seqArchR
seqs_acgt_image | Visualize all sequences as an image
write_seqArchR_cluster_track_bed | Write seqArchR cluster information in BED files viewable as browser tracks