Downstream analyses of promoter sequence architectures and HTML report generation


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Documentation for package ‘seqArchRplus’ version 1.4.0

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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