LICENSE
MANIFEST.in
README.md
setup.py
qadabra/__init__.py
qadabra/qadabra.py
qadabra/utils.py
qadabra.egg-info/PKG-INFO
qadabra.egg-info/SOURCES.txt
qadabra.egg-info/dependency_links.txt
qadabra.egg-info/entry_points.txt
qadabra.egg-info/requires.txt
qadabra.egg-info/top_level.txt
qadabra/config/config.yaml
qadabra/config/qadabra.mplstyle
qadabra/test_data/metadata.tsv
qadabra/test_data/qadabra_tutorial_metadata.tsv
qadabra/test_data/qadabra_tutorial_table.biom
qadabra/test_data/table.biom
qadabra/test_data/archive/127612_insertion_tree.relabelled.tre
qadabra/test_data/archive/obs_ids.txt
qadabra/test_data/archive/seqs.fna
qadabra/workflow/Snakefile
qadabra/workflow/data/metadata.tsv
qadabra/workflow/data/table.biom
qadabra/workflow/envs/qadabra-da-R.yaml
qadabra/workflow/envs/qadabra-default.yaml
qadabra/workflow/envs/qadabra-empress.yaml
qadabra/workflow/envs/qadabra-qurro.yaml
qadabra/workflow/envs/qadabra-songbird.yaml
qadabra/workflow/report/create_diff_table.rst
qadabra/workflow/report/create_pval_table.rst
qadabra/workflow/report/empress.rst
qadabra/workflow/report/plot_diff_kendall_heatmap.rst
qadabra/workflow/report/plot_differentials.rst
qadabra/workflow/report/plot_pca.rst
qadabra/workflow/report/plot_prc.rst
qadabra/workflow/report/plot_pvalue_kendall_heatmap.rst
qadabra/workflow/report/plot_pvalue_pw_comparisons.rst
qadabra/workflow/report/plot_pvalue_volcanoes.rst
qadabra/workflow/report/plot_rank_comparison.rst
qadabra/workflow/report/plot_rank_correlation.rst
qadabra/workflow/report/plot_roc.rst
qadabra/workflow/report/plot_upset.rst
qadabra/workflow/report/qurro.rst
qadabra/workflow/report/workflow.rst
qadabra/workflow/rules/common.smk
qadabra/workflow/rules/diffab.smk
qadabra/workflow/rules/ml.smk
qadabra/workflow/rules/visualization.smk
qadabra/workflow/scripts/concatenate_all_results.py
qadabra/workflow/scripts/concatenate_differentials.py
qadabra/workflow/scripts/concatenate_pvalues.py
qadabra/workflow/scripts/create_diff_table.py
qadabra/workflow/scripts/create_pval_table.py
qadabra/workflow/scripts/get_log_ratios.py
qadabra/workflow/scripts/get_pctile_feats.py
qadabra/workflow/scripts/logistic_regression.py
qadabra/workflow/scripts/plot_diff_kendall_heatmap.py
qadabra/workflow/scripts/plot_differentials.py
qadabra/workflow/scripts/plot_pca.py
qadabra/workflow/scripts/plot_prc.py
qadabra/workflow/scripts/plot_pvalue_kendall_heatmap.py
qadabra/workflow/scripts/plot_pvalue_pw_comparisons.py
qadabra/workflow/scripts/plot_pvalue_volcanoes.py
qadabra/workflow/scripts/plot_rank_comparison.py
qadabra/workflow/scripts/plot_roc.py
qadabra/workflow/scripts/plot_upset.py
qadabra/workflow/scripts/process_differentials.py
qadabra/workflow/scripts/process_pvalues.py
qadabra/workflow/scripts/run_pca.py
qadabra/workflow/scripts/R/aldex2.R
qadabra/workflow/scripts/R/ancombc.R
qadabra/workflow/scripts/R/corncob.R
qadabra/workflow/scripts/R/deseq2.R
qadabra/workflow/scripts/R/edger.R
qadabra/workflow/scripts/R/maaslin2.R
qadabra/workflow/scripts/R/metagenomeseq.R