Package index
-
plot_alpha_diversity()
- Plot Alpha Diversity
-
generate_alpha_boxplot_single()
- Generate boxplot for alpha diversity index at a single time point
-
generate_alpha_boxplot_long()
- Generate boxplot for specified alpha diversity index
-
generate_alpha_per_time_dotplot_long()
- Longitudinal Alpha Diversity Dot Plot for Microbiome Data
-
generate_alpha_spaghettiplot_long()
- Generate an alpha diversity line plot for longitudinal data
-
generate_alpha_change_boxplot_pair()
- Generate boxplot comparing change in specified alpha diversity index
-
generate_alpha_change_test_pair()
- Compare alpha diversity between time points
-
generate_alpha_change_per_time_test_long()
- Compare alpha diversity between time points
-
generate_alpha_test_pair()
- Alpha Diversity Association Test
-
generate_alpha_per_time_test_long()
- Longitudinal Alpha Diversity Test in Microbiome Data
-
generate_alpha_test_single()
- Perform alpha diversity association tests using linear models
-
generate_alpha_trend_test_long()
- Longitudinal Alpha Diversity Trend Test in MicrobiomeStat
-
generate_alpha_volatility_test_long()
- Longitudinal Alpha Diversity Volatility Test in MicrobiomeStat
-
mStat_calculate_adjusted_alpha_diversity()
- Adjust Alpha Diversity Indices Based on Covariates
-
is_rarefied()
- Check if the data has been rarefied
-
plot_beta_diversity()
- Plot Beta Diversity
-
generate_beta_change_boxplot_pair()
- Compare beta diversity between time points
-
generate_beta_change_boxplot_long()
- Compare within-group and between-group beta diversity across time points
-
generate_beta_change_spaghettiplot_long()
- Generate beta diversity change spaghetti plot for longitudinal data
-
generate_beta_ordination_long()
- Generate Beta Ordination Plots
-
generate_beta_ordination_pair()
- Generate beta ordination plots for paired samples
-
generate_beta_ordination_single()
- Generate Beta Diversity Ordination Plot
-
generate_beta_pc_change_boxplot_pair()
- Visualize Beta Diversity Changes Over Time
-
generate_beta_change_test_pair()
- Compute and analyze changes in beta diversity
-
generate_beta_change_per_time_test_long()
- Generate Beta Change Tests for Longitudinal Data
-
generate_beta_per_time_dotplot_long()
- Longitudinal Beta Diversity Dot Plot for Microbiome Data
-
generate_beta_pc_boxplot_long()
- Create Boxplots for Beta Diversity Metrics
-
generate_beta_pc_spaghettiplot_long()
- Generate spaghetti plots of beta diversity over time
-
generate_beta_pc_trend_test_long()
- Trend Test on Principal Coordinates of Beta Diversity Metrics Over Time
-
generate_beta_pc_volatility_test_long()
- Generate Beta PC Volatility Test in Long Format
-
generate_beta_test_single()
- Calculate Beta Diversity Indices and Perform PERMANOVA Tests
-
generate_beta_trend_test_long()
- Generate Beta Diversity Trend Test for Longitudinal Data
-
generate_beta_volatility_test_long()
- Generate Beta Diversity Volatility Test for Longitudinal Data
-
mStat_calculate_adjusted_distance()
- Calculate Adjusted Distances for Specified Variables
-
mStat_calculate_PC()
- Calculate Principal Coordinates using MDS, NMDS
-
plot_feature_diversity()
- Visualize the relative abundance of selected taxa or functions
-
generate_taxa_cladogram_single()
- Generate a Circular Cladogram with Heatmap for Taxa
-
generate_taxa_barplot_pair()
- Generate Pairwise Taxa Barplots for Longitudinal Data
-
generate_taxa_barplot_single()
- Generate Stacked Taxa Barplots for Single or Longitudinal Data
-
generate_taxa_boxplot_long()
- Generate Taxa Boxplots for Longitudinal Data
-
generate_taxa_boxplot_single()
- Generate Single Time Point Taxa Boxplots
-
generate_taxa_change_dotplot_pair()
- Generate Taxa Stack Dotplot Pair
-
generate_taxa_change_heatmap_long()
- Generate Taxonomic Change Heatmap Long
-
generate_taxa_change_heatmap_pair()
- Generate Taxa Change Heatmap Pair
-
generate_taxa_change_scatterplot_pair()
- Generate taxa-level difference scatterplot pairs
-
generate_taxa_dotplot_pair()
- Generate Taxa Stack Dotplot Pair
-
generate_taxa_dotplot_single()
- Generate Taxonomic Dotplot Single
-
generate_taxa_heatmap_long()
- Generate Taxonomic Heatmap Long
-
generate_taxa_heatmap_pair()
- Generate Taxonomic Heatmap Pair
-
generate_taxa_heatmap_single()
- Generate Taxonomic Heatmap Single
-
generate_taxa_areaplot_long()
- Generate taxa area plots over time
-
generate_taxa_barplot_long()
- Generate Taxa Barplots for Longitudinal Data
-
generate_taxa_per_time_dotplot_long()
- Longitudinal Taxa Dot Plot for Microbiome Data
-
generate_taxa_change_boxplot_pair()
- Generate Individual Taxa Change Boxplot Pair
-
generate_taxa_change_test_pair()
- Compute taxa changes and analyze differential abundance
-
generate_taxa_change_per_time_test_long()
- Longitudinal Taxa Test in Microbiome Data
-
generate_taxa_indiv_boxplot_long()
- Generate Boxplot of Individual Taxa Abundance Over Time
-
generate_taxa_indiv_boxplot_single()
- Generate Taxa Boxplots for Single Time Point
-
generate_taxa_indiv_change_boxplot_pair()
- Generate Individual Change Boxplot Pairs for Taxonomic Composition Data
-
generate_taxa_indiv_change_scatterplot_pair()
- Generate Individual Change Scatterplot Pairs for Taxonomic Composition Data
-
generate_taxa_indiv_spaghettiplot_long()
- Generate longitudinal line plots of taxonomic composition
-
generate_taxa_spaghettiplot_long()
- Generate longitudinal spaghettiplot plots of taxonomic composition
-
generate_taxa_test_pair()
- Generate Taxa Test Pair
-
generate_taxa_per_time_test_long()
- Longitudinal Differential Abundance Test in Microbiome Data
-
generate_taxa_test_single()
- Conduct Differential Abundance Testing Using LinDA Method in MicrobiomeStat Package
-
generate_taxa_volcano_single()
- Generate Volcano Plots for Taxa Differential Test for a Single Time Point
-
generate_taxa_association_test_long()
- Longitudinal Taxa Association Test Generation
-
generate_taxa_trend_test_long()
- Longitudinal Taxa Trend Test Generation
-
generate_taxa_trend_volcano_long()
- Generate Volcano Plots for Longitudinal Taxa Trend Test
-
generate_taxa_volatility_test_long()
- Longitudinal Taxa Abundance Volatility Test
-
generate_taxa_volatility_volcano_long()
- Generate Volcano Plots for Longitudinal Taxa Abundance Volatility Test
-
mStat_aggregate_by_taxonomy()
- Aggregate OTU Table by Taxonomy Level
-
mStat_aggregate_by_taxonomy2()
- Aggregate OTU Table by Taxonomy Level
-
mStat_subset_alpha()
- Subset Alpha Diversity Object
-
mStat_subset_dist()
- Subset Distance Matrix
-
mStat_subset_PC()
- Subset Principal Coordinates Analysis (PCoA) Results
-
mStat_summarize_data_obj()
- Summarize a MicrobiomeStat Data Object
-
mStat_process_time_variable()
- Handle Time Variable in Meta Data Table
-
mStat_convert_DESeqDataSet_to_data_obj()
- Convert a DESeqDataSet Object to a MicrobiomeStat Data Object
-
mStat_convert_DGEList_to_data_obj()
- Convert a DGEList Object to a MicrobiomeStat Data Object
-
mStat_convert_MRExperiment_to_data_obj()
- Convert a MRExperiment Object to a MicrobiomeStat Data Object
-
mStat_convert_MultiAssayExperiment_to_data_obj()
- Convert MultiAssayExperiment Object to a Data Object
-
mStat_convert_phyloseq_to_data_obj()
- Convert a Phyloseq Object to a MicrobiomeStat's Data Object
-
mStat_convert_SummarizedExperiment_to_data_obj()
- Convert SummarizedExperiment Object to a MicrobiomeStat Data Object
-
mStat_import_biom_as_data_obj()
- Import a BIOM formatted data file into an mStat data object
-
mStat_import_dada2_as_data_obj()
- Convert DADA2 Data into MicrobiomeStat's Data Object
-
mStat_import_mothur_as_data_obj()
- Convert Mothur Data into MicrobiomeStat's Data Object
-
mStat_import_qiime2_as_data_obj()
- Convert Qiime2 Data into MicrobiomeStat's Data Object
-
mStat_normalize_data()
- Normalize a MicrobiomeStat Data Object
-
mStat_rarefy_data()
- Rarefy data to a specified sampling depth
-
mStat_filter()
- Filter a Microbiome Data Matrix by Prevalence and Average Abundance
-
mStat_remove_feature()
- Remove Specific Features from a MicrobiomeStat Data Object
-
mStat_subset_data()
- Subset Data Object by Sample IDs in MicrobiomeStat
-
mStat_update_meta_data()
- Update Metadata in a MicrobiomeStat Data Object
-
mStat_update_sample_name()
- Update Sample Names in MicrobiomeStat Data Object
-
mStat_validate_data()
- Validate and Adjust a MicrobiomeStat Data Object
-
mStat_identify_time_varying_vars()
- Identify Time-Varying Variables within Subjects
-
mStat_generate_report_long()
- Generate Comprehensive Longitudinal Microbiome Analysis Report for MicrobiomeStat
-
mStat_generate_report_pair()
- Generate a report for microbial ecology analysis of paired data
-
mStat_generate_report_single()
- Generate a report for microbial ecology analysis of cross-sectional, longitudinal or paired data at a single time point
-
ecam.obj
- Data from the Early Childhood Antibiotics and the Microbiome (ECAM) study
-
peerj32.obj
- Probiotics Intervention Data from the PeerJ32 Study
-
smokers
- Smokers Microbiome Data from the Human Upper Respiratory Tract
-
subset_T2D.obj
- Subset T2D Microbiome Data from the HMP2 Study
-
subset_pairs.obj
- Paired Sample 16S Sequencing Data from the MiPair Study
-
mStat_get_palette()
- Retrieve Custom Color Palettes for Data Visualization
-
mStat_get_theme()
- Get the ggplot2 Theme for Plots
-
is_categorical()
- Determine if a variable is categorical
-
is_continuous_numeric()
- Check if a Variable is Continuous Numeric
-
linda.plot()
- Plot linda results
-
build_mStat_tax_table()
- Build mStat tax table
-
mStat_aggregate_data()
- Aggregate Data Function
-
linda()
- Linear (Lin) model for differential abundance (DA) analysis
-
mStat_calculate_alpha_diversity()
- Calculate alpha diversity indices
-
mStat_calculate_beta_diversity()
- Calculate various beta diversity indices
-
mStat_combine_data()
- mStat_combine_data