NEWS

seqArchRplus 1.1.3

(User-facing) Ability to generate HTML reports to view large combined panels for multiple processed samples as scrollable carousels

(User-facing) Alternative function plot_motif_heatmaps2() combines the heatmap scale with the heatmaps. Also, can choose to output PNG or JPEG files

(User-facing) An alternative function to plot motif heatmaps using the R pkg seqPattern. Function name: plot_motif_heatmaps2()

(User-facing) Now possible to perform per cluster GO term enrichment analysis via per_cluster_go_term_enrichments() when a orgDb package is available for the organism

(User-facing) In per_cluster_annotations():
- Default for clusts set to NULL. This enables cleanly specifying just the BED file as input to tc_gr
- Help pages now have examples except for the curate_clusters function. Elaborate documentation for this function is available as part of the vignette

(User-facing) In write_seqArchR_cluster_track_bed():
- new argument use_q_bound to choose if you wish to use quantiles as tag cluster boundaries
- new argument use_as_names to specify any column in info_df to be used as the name column in the output track BED file of clusters
- dominant_ctss information for each tag cluster is presented as thickStart thickEnd for ease of visualising. See documentation for more details
(User-facing) In per_cluster_annotations():
- tc_gr can now accept a bedfile to read records as a GRanges object
- Details added in documentation for ways to selectively pick clusters to annotate