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_pkgdown.yml
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url: https://cparsania.github.io/parcutils/
template:
bootstrap: 5
reference:
- title: "RNA-seq related"
contents:
- get_star_align_log_summary
- normalise_counts
- run_deseq_analysis
- get_fold_change_matrix
- get_normalised_expression_matrix
- get_genes_by_regulation
- get_go_emap_plot
- save_go_data
- save_go_plots
- gsea_analysis
- enrichMsigDB
- gseMsigDB
- title: "Visualization related"
contents:
- get_pairwise_corr_plot
- get_corr_heatbox
- get_gene_expression_box_plot
- get_gene_expression_heatmap
- get_fold_change_heatmap
- get_heatmap_data
- get_pca_plot
- get_upset_intersects
- EnhancedVolcano2
- get_volcano_plot
- plot_deg_upsets
- plot_regions_relative_to_reference
- get_star_align_log_summary_plot
- get_diff_gene_count_barplot
- get_gene_expression_line_plot
- get_fold_change_line_plot
- get_fold_change_scatter_plot
- plot_deg_venn
- title: "Others"
contents:
- get_intergenic_signals
- named_group_split
- sort_geom_box
- ggsave2
- title: "SpliceWiz related"
contents:
- get_ASE_counts_barplot
- run_ase_diff_analysis
- get_diff_ASE_count_barplot
- get_ASE_data_matrix
- get_ase_data_matrix_heatmap
- get_genes_from_event_name
- event_region_to_granges
- get_ASEsets_by_regulation
- get_ase_volcano_plot
- event_region_to_coordinate
- get_event_annotations
- plot_deASE_venn
- title: "ChIP related"
contents:
- make_parcutils_chip
- normalised_matrix_to_rpm
- import_topn_bed_features
- make_enriched_heatmap_list
- get_chip_signal_heatmap
- get_chip_signal_over_control_heatmap
- get_five_prime_flank_motif
- get_three_prime_flank_motif
- plot_chip_pairwise_correlation_heatmap
# figures:
# dev: ragg::agg_png
# dpi: 96
# dev.args: []
# fig.ext: png
# fig.width: 7.2916667
# fig.height: ~
# fig.retina: 2
# fig.asp: 1.618
# bg: NA
# other.parameters: []