Man pages for EESI/themetagenomics
Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data
| cnn | Normalize an OTU table by 16S rRNA copy number |
| DAVID | Human longitudinal microbiome data |
| download_ref | Download functional prediction reference tables |
| est | Estimate topic or function effects |
| est.functions | Estimate predicted function-topic effects |
| est.topics | Estimate topic effects |
| est_topics_backend | Backend to extract effects for 'est.topics'. |
| extract | Extract summary statistics |
| extract_stan_summary | Backend to extract summary from rstan object |
| find_topics | Perform topic estimation on a themetadata object |
| GEVERS | Inflammatory bowel disease gut microbiome data |
| picrust | Predict OTU functional content via PICRUSt |
| picrust_otu | Predict OTU functional potential via PICRUSt |
| predict.topics | Predict topic functional content |
| prepare_data | Prepare themetadata object from data for topic modeling... |
| resume | Resume HMC using a previous fit |
| s | Make a B-spline Basis Function (from 's') |
| stm_wrapper | Wrapper for stm |
| t4f | Predict taxonomic functional content via tax4fun |
| vis | Launch in interactive visualize to explore topic effects |
