Man pages for PoonLab/clustuneR
Molecular clustering implementation and predictive optimization
| alignment.ex | An alignment of HIV1, subtype B sequences |
| annotate.growth | Add the growth information onto the known tree. |
| annotate.nodes | Prepare nodes in tree for clustering |
| annotate.paths | Get paths relative to starting nodes |
| cluster.ex | An example set of clusters, built using component.cluster |
| component.cluster | Create clusters based on the components of a graph |
| extended.tree.ex | An extension of an ape tree object which can be used to... |
| extend.tree | Place new sequences on the tree. This function makes calls to... |
| fit.analysis | Predictive analysis on clusters |
| fit.decay | Fit binomial regression model to distribution of bipartite... |
| full.tree.ex | A tree built from alignment.ex |
| generate.all | Generate data found in /data folder |
| generate.cluster | Create example cluster set |
| generate.graph | Create example graphs |
| generate.seq.info | Obtain basic sequence information |
| generate.tree | Create example trees |
| get.AIC | Get AIC values from an analysis |
| graph.ex | An example graph, built based on pairwise TN93 distances |
| import.tree | Prepare a tree for clustering analysis |
| minimum.retrospective.edge | The default growth resolution helper. |
| mono.pat.cluster | Obtain monophyletic clusters based on pairwise distances |
| multi.cluster | Wrapper for cluster.method functions |
| old.tree.ex | A tree built based on a subset of alignment.ex |
| parse.headers | Convenience function to parse metadata from sequence headers |
| read.edges | Makes a graph object based on sequence data and pairwise... |
| run.pplacer_guppy | obtain placement information to identify grown phylogenies |
| seq.info.ex | An example set of sequence meta.data corresponding to... |
| step.cluster | Obtain paraphyletic clusters |
| taxit.create | Create a refpkg |
| translate.log | Build a stats.json |
