Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data


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Documentation for package ‘themetagenomics’ version 0.1.0

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cnn Normalize an OTU table by 16S rRNA copy number
DAVID Human logitudinal microbiome data
download_ref Download functional prediction reference tables
est Estimate topic or function effects
est.functions Estimate predicted function-topic effects
est.hmc Estimate predicted function-topic effects
est.ml Estimate predicted function-topic effects
est.topics Estimate topic effects
est_functions Estimate predicted function-topic effects
est_topics Estimate topic effects
extract Extract summary statistics
extract.effects Extract summary statistics
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.functions Predict topic functional content
predict.topics Predict topic functional content
predict_functions Predict topic functional content
predict_topics Predict topic functional content
prepare_data Prepare themetadata object from data for topic modeling pipeline
resume Resume HMC using a previous fit
resume.effects Resume HMC using a previous fit
s Make a B-spline Basis Function (from 's')
t4f Predict taxonomic functional content via tax4fun
vis Launch in interactive visualize to explore topic effects
vis.binary Launch in interactive visualize to explore topic effects
vis.continuous Launch in interactive visualize to explore topic effects
vis.effects Launch in interactive visualize to explore topic effects
vis.functions Launch in interactive visualize to explore topic effects
vis.taxa Launch in interactive visualize to explore topic effects
vis.topics Launch in interactive visualize to explore topic effects