q2-fmt

qiime2

Quickstart install for:

[Fresh Install]

[Update Existing]

conda env create --name q2-fmt-amplicon-2024.10 --file https://raw.githubusercontent.com/qiime2/q2-fmt/refs/heads/dev/environment-files/q2-fmt-qiime2-amplicon-2024.10.yml

This QIIME 2 plugin supports FMT analyses.

version: 2024.11.1+8.g8ff6ad7
website: https://github.com/qiime2/q2-fmt
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
group-timepoints	method	Prep Method for organizing metadata and diversity metrics for appropriate statisics
pedf	method	Proportional Engraftment of Donor Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PEDS. PEDF uses the same ideas but is applied to features generally.
prdf	method	Porportion of Recipients with Donor Feature
pprf	method	Proportional Persistence of Recipient Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PPRS. PPRF uses the same ideas but is applied to features generally.
pedf-permutation-test	method	PEDF permutation Test
heatmap	visualizer	Proportional Features Heatmap
cc	pipeline	Pipeline for FMT Diversity Community Coalescence Analysis
detect-donor-indicators	pipeline	Detect Donor Indicator Features

This QIIME 2 plugin supports FMT analyses.

version: 2024.11.1+8.g8ff6ad7
website: https://github.com/qiime2/q2-fmt
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
group-timepoints	method	Prep Method for organizing metadata and diversity metrics for appropriate statisics
pedf	method	Proportional Engraftment of Donor Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PEDS. PEDF uses the same ideas but is applied to features generally.
prdf	method	Porportion of Recipients with Donor Feature
pprf	method	Proportional Persistence of Recipient Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PPRS. PPRF uses the same ideas but is applied to features generally.
pedf-permutation-test	method	PEDF permutation Test
heatmap	visualizer	Proportional Features Heatmap
cc	pipeline	Pipeline for FMT Diversity Community Coalescence Analysis
detect-donor-indicators	pipeline	Detect Donor Indicator Features

This QIIME 2 plugin supports FMT analyses.

version: 2024.11.1+8.g8ff6ad7
website: https://github.com/qiime2/q2-fmt
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
group-timepoints	method	Prep Method for organizing metadata and diversity metrics for appropriate statisics
pedf	method	Proportional Engraftment of Donor Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PEDS. PEDF uses the same ideas but is applied to features generally.
prdf	method	Porportion of Recipients with Donor Feature
pprf	method	Proportional Persistence of Recipient Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PPRS. PPRF uses the same ideas but is applied to features generally.
pedf-permutation-test	method	PEDF permutation Test
heatmap	visualizer	Proportional Features Heatmap
cc	pipeline	Pipeline for FMT Diversity Community Coalescence Analysis
detect-donor-indicators	pipeline	Detect Donor Indicator Features

This QIIME 2 plugin supports FMT analyses.

version: 2024.11.1+8.g8ff6ad7
website: https://github.com/qiime2/q2-fmt
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Actions¶

Name	Type	Short Description
group-timepoints	method	Prep Method for organizing metadata and diversity metrics for appropriate statisics
pedf	method	Proportional Engraftment of Donor Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PEDS. PEDF uses the same ideas but is applied to features generally.
prdf	method	Porportion of Recipients with Donor Feature
pprf	method	Proportional Persistence of Recipient Features in each recipient sample. This is adapted from aggarwala et al. 2021 stainer manuscript, which coined the term PPRS. PPRF uses the same ideas but is applied to features generally.
pedf-permutation-test	method	PEDF permutation Test
heatmap	visualizer	Proportional Features Heatmap
cc	pipeline	Pipeline for FMT Diversity Community Coalescence Analysis
detect-donor-indicators	pipeline	Detect Donor Indicator Features

Links

Documentation

Source Code

Stars

Last Commit

8ff6ad7

Available Distros

2024.10: 2024.10/amplicon