Files in qpmnguyen/microbe_set_trait
Reproducible analyses for evaluating trait-based taxon sets
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DESCRIPTION
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R/concordance_functions.R
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R/functions_coverage.R
R/functions_pred.R
R/generate_scores.R
R/generate_scores_func.R
R/metaphlan_db.R
R/name_2_ncbi_id.R
R/plot_coverage.R
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R/utils.R
README.md
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data/condensed_species_NCBI.txt
data/madin_proc.rds
data/pred_pathway_crc_feat.csv
data/pred_pathway_crc_metadata.csv
data/pred_pathway_ibd_feat.csv
data/pred_pathway_ibd_metadata.csv
data/pred_picrust2_crc_feat.csv
data/pred_picrust2_crc_metadata.csv
data/pred_picrust2_ibd_feat.csv
data/pred_picrust2_ibd_metadata.csv
data/pred_relabun_crc_16s.rds
data/pred_relabun_crc_wgs.rds
data/pred_relabun_ibd_16s.rds
data/pred_relabun_ibd_wgs.rds
data/trait_crc_16s_feat.csv
data/trait_crc_wgs_feat.csv
data/trait_ibd_16s_feat.csv
data/trait_ibd_wgs_feat.csv
data/weissman.csv
docs/Rplot001.ps
docs/coverage.ipynb
docs/crc_16s_manifest.ipynb
docs/db_prep.ipynb
docs/discovering_16s_data.ipynb
docs/export_16s.ipynb
docs/export_16s_picrust2.ipynb
docs/exporting_wgs.ipynb
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docs/hmp_16s_read_preprocessing.ipynb
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docs/predicive_modelling.ipynb
docs/prediction.html
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microbe_set_trait.Rproj
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output/sets/set_substrate_species.rds
pid_nohup.txt
pred_job.sh
python/__init__.py
python/__pycache__/pred_eval.cpython-39.pyc
python/crc_16s.tsv
python/download_crc.py
python/download_hmp.py
python/feature_importance.py
python/hmp_16s.csv
python/hmp_16s.txt
python/hmp_urls.csv
python/metacyc.py
python/picrust2_qiime.py
python/pred_eval.py
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
run.R
run_individual.sh
run_slurm.sh
workflow/env/microbe_trait_env.yml
workflow/env/picrust_env.yml
workflow/env/predictive_analysis.yml
workflow/env/qiime2-2022.2-py38-linux-conda.yml
workflow/env/using_r.yml
workflow/rules/coverage.smk
workflow/rules/dada2.smk
workflow/rules/db2set.smk
workflow/rules/db_prep.smk
workflow/rules/feat_importance.smk
workflow/rules/picrust.smk
workflow/rules/pred.smk
workflow/rules/trait_scores.smk
