qiime2 / q2-diversity

qiime2/q2-diversity Issues

add action for filtering FeatureData[AlphaDiversity]
Closed 4 months ago2
Pre 2024.5 TSNE perplexity was not properly validated
Closed 4 months ago
The difference between the simpson and simpson_e indices
Closed 5 months ago2
BUG: more descriptive error message for too few samples retained in 'alpha-group-significance' visualization
Closed 6 months ago1
Broken link in `qiime diversity alpha` parameter description.
Updated 7 months ago
decouple file names and metadata column names
Updated 7 months ago
enable output of group distances from `beta-group-significance` for plotting with q2-vizard
Updated 7 months ago
BUG: `ignore_missing_samples` param not exposed from emperor plot in `core-metrics` and `core-metrics-phylogenetic`
Closed 8 months ago1
upgrade to adonis2
Updated 10 months ago7
Frame is cut when looking at a rarefaction plot
Closed 10 months ago3
File name too long
Closed 10 months ago7
Validating the number of samples
Updated 10 months ago
adonis: enable pairwise adonis
Updated 10 months ago
Bioenv raises a ValueError when a metadata file has columns with no values, even when other columns have values
Updated 10 months ago
Special characters in metadata groups break links to graphs
Updated a year ago5
Bray-Curtis: `Data must be symmetric and cannot contain NaNs.`
Updated a year ago2
Euclidean misbehaving
Closed a year ago1
Pip 22.0.4 pip install -e . fails
Closed a year ago1
DOCS: broken link in Adonis docs
Closed 3 years ago1
adonis: add option to ignore NaNs
Updated 4 years ago
ENH: adonis: validate metadata to check for NaNs
Closed 4 years ago5
UX Bug: `beta` allows RelativeFrequency, Type errors on RF with unsupported metrics
Updated 4 years ago4
Correct negative eigenvalues for PCoA on semi-metric distances
Updated 4 years ago
Verify ADONIS method works with R 4.0
Closed 4 years ago1
IMP: Remember ticks in 'qiime diversity alpha-rarefaction' if metric changes
Updated 4 years ago
Pielou's Evenness can produce nan, causing downstream exceptions
Updated 4 years ago3
API `n_jobs` to `thread` breaking change in #281
Closed 4 years ago3
ENH: Route all alpha and beta diversity calculations through q2-diversity-lib
Closed 4 years ago1
MAINT: Remove deprecated `alpha-phylogenetic-` methods
Closed 4 years ago
coverage < 100% in q2_diversity/_beta/_method.py
Closed 4 years ago1
`alpha` not capable of handling `lladser_ci` metric
Closed 4 years ago1
`beta` not capable of handling `wminkowski`, `mahalanobis`
Closed 4 years ago
Add tests catching table data mutations in pipelines and alpha-rarefaction
Closed 4 years ago1
more informative error message for name clashes
Closed 4 years ago4
IMP: Save plots from qiime diversity alpha-rarefaction
Updated 4 years ago3
Handle weighted version of `minkowski`
Updated 4 years ago
Reinstate `mahalanobis`
Updated 4 years ago
Reinstate `lladser_ci` with improved handling of ci Results
Updated 4 years ago
Bioenv fails if 0 variance columns are left after dropping rows with empty cells
Closed 4 years ago1
"Hand-build" test data for weighted unifrac
Updated 4 years ago
core-metrics-[phylogenetic] n-jobs is inconsistent with help text
Closed 4 years ago6
ENH: alpha_correlation should have intersect_ids parameter
Closed 5 years ago3
Flipping coordinates for biplot ordination
Closed 5 years ago3
remove step loading phylogeny as skbio.TreeNode
Closed 5 years ago
adonis: support single quotes in sample metadata
Closed 5 years ago
adonis: expose `strata` parameter for nested designs
Updated 5 years ago
Test suite fails on travis due to n_jobs tests
Closed 6 years ago
beta-group-significance: add r2 values for PERMANOVA tests
Updated 6 years ago
beta: add Yue Clayton distance metric
Updated 6 years ago
`beta-group-significance` and others: add text describing stats output
Updated 6 years ago