Man pages for wu-lab-uva/RasperGade16S
Prediction of 16S rRNA GCN with RasperGade
| align_with_HMM_and_trim | Align and trim sequence |
| check_partition | Parse grouping information |
| get_connected_nodes | Grouping connected nodes into neighborhoods |
| get_partition_AIC | Calculate AIC after partition |
| get_partition_transition | Get number of transitions |
| insert_query_with_EPA | Run EPA from R terminal |
| parse_jplace | Parse EPA results |
| partition_phylogeny | Binary partition of a phylogeny |
| predict_16SGCN_from_jplace | Predict 16S rRNA GCN from sequence placements |
| predict_16SGCN_from_sequences | Predict 16S rRNA GCN from sequences |
| RasperGade16S.GG.13.8.mask.keys | GreenGene 13.8 16S rRNA gene mask for RasperGade16S |
| RasperGade16S.refdata | Default full reference data for RasperGade16S |
| RasperGade16S.refGCN | Default reference GCN for RasperGade16S |
| RasperGade16S.reftree | Default reference tree for RasperGade16S |
| RasperGade16S.SILVA.GCN | Predicted SILVA 132 GCN (Bacteria only) by RasperGade16S |
| refine_partition | Refine partition by reverting groups |
| relative_abundance | Convert absolute abundance to relative abundance |
| rescale_tree_by_partition_and_model | Rescale tree given a partition and models |
| trim_sequence_with_mask | Trim 16S sequence based on GreenGene 13.8 16S mask |
