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_pkgdown.yml
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/
_pkgdown.yml
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# Website URL
url: https://cafferychen777.github.io/MicrobiomeStat/
# Website title
title: MicrobiomeStat
# Use Bootstrap version 5
template:
bootstrap: 5
params:
search: true # 启用基本搜索功能
bootswatch: flatly # 使用 flatly 主题
# Navigation bar settings
navbar:
type: default
right:
- icon: fa-github fa-lg
href: https://github.com/cafferychen777/MicrobiomeStat
# Reference page settings
reference:
- title: "Alpha Diversity"
contents:
- plot_alpha_diversity
- generate_alpha_boxplot_single
- generate_alpha_boxplot_long
- generate_alpha_per_time_dotplot_long
- generate_alpha_spaghettiplot_long
- generate_alpha_change_boxplot_pair
- generate_alpha_change_test_pair
- generate_alpha_change_per_time_test_long
- generate_alpha_test_pair
- generate_alpha_per_time_test_long
- generate_alpha_test_single
- generate_alpha_trend_test_long
- generate_alpha_volatility_test_long
- mStat_calculate_adjusted_alpha_diversity
- is_rarefied
- title: "Beta Diversity"
contents:
- plot_beta_diversity
- generate_beta_change_boxplot_pair
- generate_beta_change_boxplot_long
- generate_beta_change_spaghettiplot_long
- generate_beta_ordination_long
- generate_beta_ordination_pair
- generate_beta_ordination_single
- generate_beta_pc_change_boxplot_pair
- generate_beta_change_test_pair
- generate_beta_change_per_time_test_long
- generate_beta_per_time_dotplot_long
- generate_beta_pc_boxplot_long
- generate_beta_pc_spaghettiplot_long
- generate_beta_pc_trend_test_long
- generate_beta_pc_volatility_test_long
- generate_beta_test_single
- generate_beta_trend_test_long
- generate_beta_volatility_test_long
- mStat_calculate_adjusted_distance
- mStat_calculate_PC
- title: "Feature-level Analysis"
contents:
- plot_feature_diversity
- generate_taxa_cladogram_single
- generate_taxa_barplot_pair
- generate_taxa_barplot_single
- generate_taxa_boxplot_long
- generate_taxa_boxplot_single
- generate_taxa_change_dotplot_pair
- generate_taxa_change_heatmap_long
- generate_taxa_change_heatmap_pair
- generate_taxa_change_scatterplot_pair
- generate_taxa_dotplot_pair
- generate_taxa_dotplot_single
- generate_taxa_heatmap_long
- generate_taxa_heatmap_pair
- generate_taxa_heatmap_single
- generate_taxa_areaplot_long
- generate_taxa_barplot_long
- generate_taxa_per_time_dotplot_long
- generate_taxa_change_boxplot_pair
- generate_taxa_change_test_pair
- generate_taxa_change_per_time_test_long
- generate_taxa_indiv_boxplot_long
- generate_taxa_indiv_boxplot_single
- generate_taxa_indiv_change_boxplot_pair
- generate_taxa_indiv_change_scatterplot_pair
- generate_taxa_indiv_spaghettiplot_long
- generate_taxa_spaghettiplot_long
- generate_taxa_test_pair
- generate_taxa_per_time_test_long
- generate_taxa_test_single
- generate_taxa_volcano_single
- generate_taxa_association_test_long
- generate_taxa_trend_test_long
- generate_taxa_trend_volcano_long
- generate_taxa_volatility_test_long
- generate_taxa_volatility_volcano_long
- mStat_aggregate_by_taxonomy
- mStat_aggregate_by_taxonomy2
- title: "Data Management"
contents:
- mStat_subset_alpha
- mStat_subset_dist
- mStat_subset_PC
- mStat_summarize_data_obj
- mStat_process_time_variable
- mStat_convert_DESeqDataSet_to_data_obj
- mStat_convert_DGEList_to_data_obj
- mStat_convert_MRExperiment_to_data_obj
- mStat_convert_MultiAssayExperiment_to_data_obj
- mStat_convert_phyloseq_to_data_obj
- mStat_convert_SummarizedExperiment_to_data_obj
- mStat_import_biom_as_data_obj
- mStat_import_dada2_as_data_obj
- mStat_import_mothur_as_data_obj
- mStat_import_qiime2_as_data_obj
- mStat_normalize_data
- mStat_rarefy_data
- mStat_filter
- mStat_remove_feature
- mStat_subset_data
- mStat_update_meta_data
- mStat_update_sample_name
- mStat_validate_data
- mStat_identify_time_varying_vars
- title: "Reports"
contents:
- mStat_generate_report_long
- mStat_generate_report_pair
- mStat_generate_report_single
- title: "Data Sets"
contents:
- ecam.obj
- peerj32.obj
- smokers
- subset_T2D.obj
- subset_pairs.obj
- title: "Miscellaneous"
contents:
- mStat_get_palette
- mStat_get_theme
- is_categorical
- is_continuous_numeric
- linda.plot
- build_mStat_tax_table
- aggregate_data
- linda
- mStat_calculate_alpha_diversity
- mStat_calculate_beta_diversity
- mStat_combine_data