Downstream analyses of promoter sequence architectures and HTML
report generation
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Documentation for package ‘seqArchRplus’ version 1.4.0
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 |