This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
This QIIME 2 plugin supports metrics for calculating and exploring community alpha and beta diversity through statistics and visualizations in the context of sample metadata.
- version:
2024.10.0 - website: https://
github .com /qiime2 /q2 -diversity - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| pcoa | method | Principal Coordinate Analysis |
| pcoa-biplot | method | Principal Coordinate Analysis Biplot |
| tsne | method | t-distributed stochastic neighbor embedding |
| umap | method | Uniform Manifold Approximation and Projection |
| procrustes-analysis | method | Procrustes Analysis |
| partial-procrustes | method | Partial Procrustes |
| filter-distance-matrix | method | Filter samples from a distance matrix. |
| filter-alpha-diversity | method | Filter samples from an alpha diversity metric. |
| alpha-group-significance | visualizer | Alpha diversity comparisons |
| bioenv | visualizer | bioenv |
| beta-group-significance | visualizer | Beta diversity group significance |
| mantel | visualizer | Apply the Mantel test to two distance matrices |
| alpha-correlation | visualizer | Alpha diversity correlation |
| alpha-rarefaction | visualizer | Alpha rarefaction curves |
| beta-rarefaction | visualizer | Beta diversity rarefaction |
| adonis | visualizer | adonis PERMANOVA test for beta group significance |
| beta-phylogenetic | pipeline | Beta diversity (phylogenetic) |
| beta | pipeline | Beta diversity |
| alpha-phylogenetic | pipeline | Alpha diversity (phylogenetic) |
| alpha | pipeline | Alpha diversity |
| core-metrics-phylogenetic | pipeline | Core diversity metrics (phylogenetic and non-phylogenetic) |
| core-metrics | pipeline | Core diversity metrics (non-phylogenetic) |
| beta-correlation | pipeline | Beta diversity correlation |
- Links
- Documentation
- Source Code
- Stars
- 4
- Last Commit
- da384c7
- Available Distros
- 2024.10
- 2024.10/amplicon
- 2024.10/metagenome
- 2024.5
- 2024.5/amplicon
- 2024.5/metagenome
- 2024.2
- 2024.2/amplicon
- 2023.9
- 2023.9/amplicon
- 2023.7
- 2023.7/core