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.DS_Store
.DS_Store
 
 
1.1. prep_sample_info (Python).ipynb
1.1. prep_sample_info (Python).ipynb
 
 
1.2 Prepare mapping file (Python).ipynb
1.2 Prepare mapping file (Python).ipynb
 
 
1.3. Prepare biom table (Python).ipynb
1.3. Prepare biom table (Python).ipynb
 
 
1.4. SEPP Tree, Alpha, Beta, Rarefy (Qiime2).ipynb
1.4. SEPP Tree, Alpha, Beta, Rarefy (Qiime2).ipynb
 
 
2.1 Alpha Diversity Analysis -- Add to mapping file (Python).ipynb
2.1 Alpha Diversity Analysis -- Add to mapping file (Python).ipynb
 
 
2.2 Alpha Diversity Analysis -- RDA (R).ipynb
2.2 Alpha Diversity Analysis -- RDA (R).ipynb
 
 
2.3 Alpha Diversity Analysis -- MLR (R).ipynb
2.3 Alpha Diversity Analysis -- MLR (R).ipynb
 
 
3.1 Beta Diversity (UW) -- RDA (R).ipynb
3.1 Beta Diversity (UW) -- RDA (R).ipynb
 
 
3.2 Beta Diversity (UW) -- PERMANOVA (R).ipynb
3.2 Beta Diversity (UW) -- PERMANOVA (R).ipynb
 
 
3.2 Beta Diversity (UW) -- Permanova Adonis (Qiime1).ipynb
3.2 Beta Diversity (UW) -- Permanova Adonis (Qiime1).ipynb
 
 
4.1. Random Forest Classification-1,25-nested CV (Python).ipynb
4.1. Random Forest Classification-1,25-nested CV (Python).ipynb
 
 
4.2. Random Forest Classification--24,25 (Nested CV).ipynb
4.2. Random Forest Classification--24,25 (Nested CV).ipynb
 
 
4.3. Random Forest Classification--25 (Nested CV) (Python).ipynb
4.3. Random Forest Classification--25 (Nested CV) (Python).ipynb
 
 
4.4. Random Forest Classification--Ratio Activation (nested CV) (Python).ipynb
4.4. Random Forest Classification--Ratio Activation (nested CV) (Python).ipynb
 
 
4.5. Random Forest Classification--Ratio catabolism (nested CV) (Python).ipynb
4.5. Random Forest Classification--Ratio catabolism (nested CV) (Python).ipynb
 
 
5.1. Random Forest Classification-1,25 (Python).ipynb
5.1. Random Forest Classification-1,25 (Python).ipynb
 
 
5.2. Random Forest Classification--24,25.ipynb
5.2. Random Forest Classification--24,25.ipynb
 
 
5.3. Random Forest Classification--25 (Python).ipynb
5.3. Random Forest Classification--25 (Python).ipynb
 
 
5.4. Random Forest Classification--Ratio Activation (Python).ipynb
5.4. Random Forest Classification--Ratio Activation (Python).ipynb
 
 
5.5. Random Forest Classification--Ratio catabolism (Python).ipynb
5.5. Random Forest Classification--Ratio catabolism (Python).ipynb
 
 
6.1 taxonomic correlation_1,25 (Python).ipynb
6.1 taxonomic correlation_1,25 (Python).ipynb
 
 
6.2 taxonomic correlation_24,25 (Python).ipynb
6.2 taxonomic correlation_24,25 (Python).ipynb
 
 
6.3 taxonomic correlation_Ratio Activation (Python).ipynb
6.3 taxonomic correlation_Ratio Activation (Python).ipynb
 
 
7.1 examine antibiotics & sites & PPI.ipynb
7.1 examine antibiotics & sites & PPI.ipynb
 
 
7.2 examine relationship between VitD measures.ipynb
7.2 examine relationship between VitD measures.ipynb
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 

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vitamin-d

Notebooks for Vitamin D manuscript

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notebooks for MrOS Vitamin D manuscript

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1st release of MrOS VitaminD analysis code Latest
Oct 23, 2020

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