qdiv

Introduction

  • What is qdiv?
    • Key Features
  • Installation instructions
  • Data types

Example usage

  • Load and save data
    • Load and create a MicrobiomeData object
    • Save files
    • Load other types of files
  • Data management
    • Finding consensus ASVs
    • Subsetting
    • Rarefy
  • Diversity
    • Alpha diversity
    • Beta diversity
  • Plot
    • Heatmap
    • Alpha diversity profiles
    • Beta diversity
  • Null models
  • Other statistics
    • Mantel test
    • PERMANOVA
    • Bootstrap summaries of dissimilarity matrices
  • References

Core Functions

  • qdiv package
    • Overview
    • Core subpackages
      • qdiv.diversity
        • diversity
        • naive_alpha()
        • phyl_alpha()
        • func_alpha()
        • mpdq()
        • mntdq()
        • naive_beta()
        • phyl_beta()
        • func_beta()
        • bray()
        • jaccard()
        • naive_multi_beta()
        • phyl_multi_beta()
        • func_multi_beta()
        • evenness()
        • dissimilarity_by_feature()
        • beta_mpdq()
        • beta_mntdq()
      • qdiv.stats
        • stats
        • mantel()
        • permanova()
        • gower()
        • pcoa_lingoes()
        • dbrda()
        • summarize_dbrda()
        • corr()
        • bootstrap_sample_matrix()
      • qdiv.plot
        • plot
        • heatmap()
        • rarefactioncurve()
        • octave()
        • pie()
        • ordination()
        • dissimilarity_contributions()
        • phyl_tree()
        • harvey_balls()
        • alpha_diversity_profile()
        • beta_diversity_profile()
        • phylo_tree()
      • qdiv.model
        • model
        • rcq()
        • nriq()
        • ntiq()
        • beta_nriq()
        • beta_ntiq()
        • simulate_community()
        • community_sample()
        • simulate_assembly()
        • generate_interdependence_matrix()
        • make_block_tree_df()
        • make_beta_splitting_tree_df()
      • qdiv.sequences
        • sequences
        • sequence_distance_matrix()
        • tree_distance_matrix()
        • load_compressed_matrix()
        • align()
        • consensus()
        • merge_objects()
    • Main data container
      • MicrobiomeData
        • What is a data object?
        • Methods
        • Complete API reference
qdiv
  • Welcome to qdiv’s documentation!
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Welcome to qdiv’s documentation!

qdiv is a Python toolkit for microbial diversity analysis, built around the robust and intuitive Hill number framework.

Introduction

  • What is qdiv?
    • Key Features
  • Installation instructions
  • Data types

Example usage

  • Load and save data
    • Load and create a MicrobiomeData object
    • Save files
    • Load other types of files
  • Data management
    • Finding consensus ASVs
    • Subsetting
    • Rarefy
  • Diversity
    • Alpha diversity
    • Beta diversity
  • Plot
    • Heatmap
    • Alpha diversity profiles
    • Beta diversity
  • Null models
  • Other statistics
    • Mantel test
    • PERMANOVA
    • Bootstrap summaries of dissimilarity matrices
  • References

Core Functions

  • qdiv package
    • Overview
    • Core subpackages
    • Main data container
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