328 lines
9.3 KiB
Plaintext
328 lines
9.3 KiB
Plaintext
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S3method("+", "AdditiveUnit")
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export("+.AdditiveUnit")
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S3method("[", "AnnotationFunction")
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export("[.AnnotationFunction")
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S3method("[", "Heatmap")
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export("[.Heatmap")
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S3method("[", "HeatmapAnnotation")
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export("[.HeatmapAnnotation")
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S3method("[", "HeatmapList")
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export("[.HeatmapList")
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S3method("[", "SingleAnnotation")
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export("[.SingleAnnotation")
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S3method("[", "comb_mat")
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export("[.comb_mat")
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S3method("[", "gridtext")
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export("[.gridtext")
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S3method("c", "ColorMapping")
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export("c.ColorMapping")
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S3method("c", "HeatmapAnnotation")
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export("c.HeatmapAnnotation")
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S3method("dim", "Heatmap")
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export("dim.Heatmap")
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S3method("grid.draw", "Legends")
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export("grid.draw.Legends")
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S3method("height", "AnnotationFunction")
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export("height.AnnotationFunction")
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S3method("height", "Heatmap")
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export("height.Heatmap")
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S3method("height", "HeatmapAnnotation")
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export("height.HeatmapAnnotation")
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S3method("height", "HeatmapList")
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export("height.HeatmapList")
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S3method("height", "Legends")
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export("height.Legends")
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S3method("height", "SingleAnnotation")
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export("height.SingleAnnotation")
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S3method("height<-", "AnnotationFunction")
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export("height<-.AnnotationFunction")
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S3method("height<-", "HeatmapAnnotation")
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export("height<-.HeatmapAnnotation")
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S3method("height<-", "SingleAnnotation")
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export("height<-.SingleAnnotation")
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S3method("heightDetails", "annotation_axis")
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export("heightDetails.annotation_axis")
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S3method("heightDetails", "legend")
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export("heightDetails.legend")
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S3method("heightDetails", "legend_body")
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export("heightDetails.legend_body")
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S3method("heightDetails", "packed_legends")
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export("heightDetails.packed_legends")
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S3method("heightDetails", "textbox")
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export("heightDetails.textbox")
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S3method("length", "HeatmapAnnotation")
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export("length.HeatmapAnnotation")
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S3method("length", "HeatmapList")
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export("length.HeatmapList")
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S3method("names", "HeatmapAnnotation")
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export("names.HeatmapAnnotation")
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S3method("names", "HeatmapList")
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export("names.HeatmapList")
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S3method("names<-", "HeatmapAnnotation")
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export("names<-.HeatmapAnnotation")
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S3method("ncol", "Heatmap")
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export("ncol.Heatmap")
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S3method("nobs", "AnnotationFunction")
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export("nobs.AnnotationFunction")
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S3method("nobs", "HeatmapAnnotation")
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export("nobs.HeatmapAnnotation")
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S3method("nobs", "SingleAnnotation")
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export("nobs.SingleAnnotation")
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S3method("nrow", "Heatmap")
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export("nrow.Heatmap")
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S3method("plot", "Heatmap")
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export("plot.Heatmap")
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S3method("plot", "HeatmapAnnotation")
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export("plot.HeatmapAnnotation")
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S3method("plot", "HeatmapList")
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export("plot.HeatmapList")
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S3method("print", "comb_mat")
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export("print.comb_mat")
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S3method("size", "AnnotationFunction")
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export("size.AnnotationFunction")
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S3method("size", "HeatmapAnnotation")
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export("size.HeatmapAnnotation")
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S3method("size", "SingleAnnotation")
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export("size.SingleAnnotation")
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S3method("size<-", "AnnotationFunction")
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export("size<-.AnnotationFunction")
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S3method("size<-", "HeatmapAnnotation")
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export("size<-.HeatmapAnnotation")
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S3method("size<-", "SingleAnnotation")
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export("size<-.SingleAnnotation")
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S3method("str", "comb_mat")
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export("str.comb_mat")
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S3method("summary", "Heatmap")
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export("summary.Heatmap")
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S3method("summary", "HeatmapList")
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export("summary.HeatmapList")
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S3method("t", "comb_mat")
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export("t.comb_mat")
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S3method("width", "AnnotationFunction")
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export("width.AnnotationFunction")
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S3method("width", "Heatmap")
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export("width.Heatmap")
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S3method("width", "HeatmapAnnotation")
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export("width.HeatmapAnnotation")
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S3method("width", "HeatmapList")
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export("width.HeatmapList")
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S3method("width", "Legends")
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export("width.Legends")
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S3method("width", "SingleAnnotation")
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export("width.SingleAnnotation")
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S3method("width<-", "AnnotationFunction")
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export("width<-.AnnotationFunction")
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S3method("width<-", "HeatmapAnnotation")
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export("width<-.HeatmapAnnotation")
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S3method("width<-", "SingleAnnotation")
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export("width<-.SingleAnnotation")
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S3method("widthDetails", "annotation_axis")
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export("widthDetails.annotation_axis")
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S3method("widthDetails", "legend")
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export("widthDetails.legend")
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S3method("widthDetails", "legend_body")
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export("widthDetails.legend_body")
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S3method("widthDetails", "packed_legends")
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export("widthDetails.packed_legends")
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S3method("widthDetails", "textbox")
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export("widthDetails.textbox")
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export("%v%")
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export("AdditiveUnit")
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export("AnnotationFunction")
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export("ColorMapping")
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export("Heatmap")
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export("Heatmap3D")
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export("HeatmapAnnotation")
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export("HeatmapList")
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export("Legend")
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export("Legends")
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export("SingleAnnotation")
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export("UpSet")
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export("adjust_dend_by_x")
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export("alter_graphic")
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export("anno_barplot")
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export("anno_block")
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export("anno_boxplot")
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export("anno_customize")
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export("anno_density")
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export("anno_empty")
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export("anno_histogram")
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export("anno_horizon")
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export("anno_image")
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export("anno_joyplot")
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export("anno_lines")
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export("anno_link")
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export("anno_mark")
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export("anno_numeric")
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export("anno_oncoprint_barplot")
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export("anno_points")
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export("anno_simple")
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export("anno_summary")
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export("anno_text")
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export("anno_textbox")
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export("anno_zoom")
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export("annotation_axis_grob")
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export("bar3D")
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export("bin_genome")
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export("cluster_between_groups")
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export("cluster_within_group")
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export("columnAnnotation")
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export("comb_degree")
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export("comb_name")
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export("comb_size")
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export("compare_heatmap")
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export("compare_heatmap.2")
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export("compare_pheatmap")
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export("complement_size")
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export("decorate_annotation")
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export("decorate_column_dend")
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export("decorate_column_names")
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export("decorate_column_title")
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export("decorate_dend")
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export("decorate_dimnames")
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export("decorate_heatmap_body")
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export("decorate_row_dend")
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export("decorate_row_names")
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export("decorate_row_title")
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export("decorate_title")
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export("default_axis_param")
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export("default_get_type")
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export("dend_heights")
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export("dend_xy")
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export("dendrogramGrob")
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export("densityHeatmap")
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export("dist2")
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export("extract_comb")
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export("frequencyHeatmap")
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export("full_comb_code")
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export("getXY_in_parent_vp")
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export("grid.annotation_axis")
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export("grid.boxplot")
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export("grid.dendrogram")
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export("grid.textbox")
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export("gt_render")
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export("ht_global_opt")
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export("ht_opt")
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export("ht_size")
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export("is_abs_unit")
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export("list_components")
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export("list_to_matrix")
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export("make_comb_mat")
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export("max_text_height")
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export("max_text_width")
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export("merge_dendrogram")
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export("normalize_comb_mat")
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export("normalize_genomic_signals_to_bins")
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export("oncoPrint")
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export("order.comb_mat")
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export("packLegend")
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export("pheatmap")
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export("pindex")
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export("restore_matrix")
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export("rowAnnotation")
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export("row_anno_barplot")
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export("row_anno_boxplot")
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export("row_anno_density")
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export("row_anno_histogram")
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export("row_anno_points")
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export("row_anno_text")
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export("set_name")
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export("set_name<-")
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export("set_size")
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export("smartAlign2")
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export("subset_gp")
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export("subset_matrix_by_row")
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export("subset_no")
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export("subset_vector")
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export("test_alter_fun")
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export("textbox_grob")
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export("unify_mat_list")
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export("upset_left_annotation")
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export("upset_right_annotation")
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export("upset_top_annotation")
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exportClasses("AdditiveUnit")
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export("AdditiveUnit")
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exportClasses("AnnotationFunction")
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export("AnnotationFunction")
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exportClasses("ColorMapping")
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export("ColorMapping")
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exportClasses("Heatmap")
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export("Heatmap")
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exportClasses("HeatmapAnnotation")
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export("HeatmapAnnotation")
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exportClasses("HeatmapList")
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export("HeatmapList")
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exportClasses("Legends")
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export("Legends")
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exportClasses("SingleAnnotation")
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export("SingleAnnotation")
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exportMethods("add_heatmap")
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exportMethods("adjust_heatmap_list")
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exportMethods("annotation_legend_size")
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exportMethods("attach_annotation")
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exportMethods("color_mapping_legend")
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exportMethods("column_dend")
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exportMethods("column_order")
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exportMethods("component_height")
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exportMethods("component_width")
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exportMethods("copy_all")
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exportMethods("draw")
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exportMethods("draw_annotation")
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exportMethods("draw_annotation_legend")
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exportMethods("draw_dend")
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exportMethods("draw_dimnames")
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exportMethods("draw_heatmap_body")
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exportMethods("draw_heatmap_legend")
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exportMethods("draw_heatmap_list")
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exportMethods("draw_title")
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exportMethods("get_color_mapping_list")
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exportMethods("get_legend_param_list")
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exportMethods("heatmap_legend_size")
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exportMethods("make_column_cluster")
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exportMethods("make_layout")
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exportMethods("make_row_cluster")
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exportMethods("map_to_colors")
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exportMethods("prepare")
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exportMethods("re_size")
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exportMethods("row_dend")
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exportMethods("row_order")
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exportMethods("set_component_height")
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exportMethods("set_component_width")
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import(digest)
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import(doParallel)
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import(foreach)
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import(grDevices)
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import(graphics)
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import(grid)
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import(matrixStats)
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import(methods)
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import(parallel)
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import(png)
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import(stats)
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importFrom("GetoptLong", qq)
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importFrom("GetoptLong", qq.options)
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importFrom("GetoptLong", qqcat)
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importFrom("GlobalOptions", setGlobalOptions)
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importFrom("IRanges", "IntegerList")
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importFrom("RColorBrewer", brewer.pal)
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importFrom("circlize", add_transparency)
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importFrom("circlize", colorRamp2)
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importFrom("circlize", rand_color)
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importFrom("circlize", smartAlign)
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importFrom("clue", as.cl_hard_partition)
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importFrom("clue", cl_class_ids)
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importFrom("clue", cl_consensus)
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importFrom("clue", cl_ensemble)
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importFrom("codetools", "findGlobals")
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importFrom("colorspace", RGB)
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importFrom("colorspace", coords)
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importFrom("colorspace", diverge_hcl)
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importFrom("colorspace", rainbow_hcl)
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importFrom("colorspace", sequential_hcl)
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importFrom("utils", "combn")
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importFrom("utils", "getFromNamespace")
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importFrom("utils", "packageDescription")
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importFrom("utils", "str")
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