q2-fmt

What’s Changed¶

*We fixed a bug that caused an numpy error in qiime fmt ped-permutation-test

• BUG: samples dropped by rarefying are in the table when mismatched pairs are made. by @cherman2 in #117

Full Changelog: #2024.11.0...2024.11.1

This is q2-fmt’s official Beta Release! Here we present all the methods needed for assessing engraftment extent following FMT. 🎉

New Actions include:

1. PEDF (Proportional Engraftment of Donor Features)
2. PEDF-permutation-test
3. PPRF (Proportion of Persistent Recipient Features)
4. PRDF (Proportion of Recipients with Donor Features)
5. Detect-donor-indicators
6. a heatmap Visualization!

For more info be sure to checkout our offical tutorial! https://q2-fmt.readthedocs.io/en/latest/intro.html If you have any questions please reach out on the q2-forum! https://forum.qiime2.org/

What’s Changed¶

• NEW: PEDS method, Heatmap VIZ and Associated Unit tests by @cherman2 in #39
• NEW: refactor for sample peds for implementation of Feature peds by @cherman2 in #48
• REF: Refactoring peds-heatmap and the peds pipeline to split taxonomic labels by @cherman2 in #68
• Update: q2-fmt to py3.9 by @cherman2 in #76
• REF: group-timepoints/engraftment pipeline take to_baseline param by @cherman2 in #71
• REF: Adds 4th dimension of Sample_Size to Heatmap by @cherman2 in #79
• REF: group-timepoints to create Dist1D[nestedOrdered] by @cherman2 in #78
• REF: Add choices to to_distance parameter by @cherman2 in #83
• NEW: Added command descriptions to q2-fmt command by @cherman2 in #75
• REF: engraftment to CC by @cherman2 in #88
• NEW: peds-simulation action by @cherman2 in #58
• BUG: Fixes bug were fdr correction was handed an float instead of a list. by @cherman2 in #90
• REF: Add more bumpers and tests to cc --to-baseline by @cherman2 in #89
• REF: minor fixes from working with Jeff by @cherman2 in #91
• REF: q2-fmt ci by @cherman2 in #92
• NEW: goodies for library by @cherman2 in #98
• NEW: PPRS action by @cherman2 in #86
• REF: q2-fmt tutorial fixes by @cherman2 in #99
• BUG: title is metadata.index.name by @cherman2 in #102
• Reformat for new library spec by @Oddant1 in #103
• REF: updates to be compatible with q2-stats by @cherman2 in #104
• add content for readthedocs builds by @gregcaporaso in #105
• add templated Jupyter Book by @gregcaporaso in #106
• ADD: detect donor indicators pipeline by @cherman2 in #109
• REF: PEDs/PEDS Associated Methods by @cherman2 in #101
• Reformat example data away from frictionless by @ebolyen in #110
• creating q2-Fmt tutorial by @cherman2 in #107
• MAINT: Rename sample-peds, feature-peds, pprs and peds-simulation by @cherman2 in #111
• fixes q2-fmt tutorial by @cherman2 in #112
• Update _config.yml by @cherman2 in #113

Full Changelog: #2023.5.0...2024.11

What’s Changed¶

• FEAT/IMP: refactoring group_timepoints and adding mann-whitney & wilcoxon significance tests by @lizgehret in #1
• FEAT: adding raincloud plot viz by @lizgehret in #3
• NEW: raincloud plots by @ebolyen in #5
• IMP: adding engraftment pipeline by @lizgehret in #4
• IMP: add stats table to rainclouds by @ebolyen in #7
• TEST: adding unit tests and usage examples for wilcoxon method and engraftment pipeline by @lizgehret in #6
• ex: working usage example for mann-whitney-u by @lizgehret in #8
• TEST: stats unit tests for mann-whitney-u and wilcoxon-srt by @lizgehret in #11
• LINT/CI: adding ci and linting cleanup by @lizgehret in #17

New Contributors¶

• @lizgehret made their first contribution in #1
• @ebolyen made their first contribution in #5

Full Changelog: https://github.com/qiime2/q2-fmt/commits/0.1.dev0