Package index
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GAnnoVizApp() - Launch GAnnoViz Shiny application
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retrieve_ensembl_species() - List Supported Species from Ensembl
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retrieve_ensembl_gff3() - Download GFF3 Annotation from Ensembl
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extract_promoters() - Extract promoter ranges from GFF or GTF
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extract_utr5() - Extract 5'UTR ranges from GFF or GTF
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extract_genes() - Extract genes information from GFF or GTF
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extract_mrnas() - Extract mRNA transcripts from GFF or GTF
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extract_cds() - Extract CDS ranges from GFF or GTF
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extract_exons() - Extract Exons ranges from GFF or GTF
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extract_utr3() - Extract 3'UTR ranges from GFF or GTF
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plot_gene_stats() - Plot gene stats for chromosomes
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plot_gene_structure() - Plot gene structure (Promoter, 3'UTR, Exon, Intron, 5'UTR)
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plot_gene_domains() - Plot protein domains from Ensembl
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plot_interval_structure() - Plot gene structures for a genomic interval
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plot_interval_flank() - Gene neighborhood architecture around a focal gene
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plot_chrom_structure() - Plot chromosome structures and gene stats
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plot_chrom_genes() - Plot chromosome structures and gene annotation
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plot_chrom_heatmap() - Plot genomic feature density heatmap
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anno_deg_chrom() - Annotate differentially expressed genes (DEGs) with chromosome positions
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plot_deg_chrom() - Plot differentially expressed genes (DEGs) hyper/hypo distributions by chromosome
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plot_deg_exp() - Plot DEGs up/down along chromosomes
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plot_deg_volcano() - Plot differentially expressed genes (DEGs) volcano
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anno_fst_dmr() - Annotate FST/DMR slide windows with genomic features
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plot_snp_density() - Plot SNP density at chromosome level
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plot_snp_fst() - Plot genomic weighted FST heatmap
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plot_snp_anno() - Plot genomic FST with Top-N gene annotations
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anno_fst_dmr() - Annotate FST/DMR slide windows with genomic features
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plot_dmg_chrom() - Plot differentially methylated regions (DMRs) hyper/hypo distributions by chromosome
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plot_dmg_exp() - Plot DMGs hyper/hypo along chromosomes
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plot_dmg_circos() - Plot DMGs circos across chromosomes
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plot_dmg_manhattan() - Plot DMGs manhattan plot across chromosomes
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plot_dmg_trend() - Plot chromosomal DMGs trend