Man pages for phraber/lassie
Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment
| aa.col | Color Look-up-Table |
| CH505 | Within-host longitudinal Env single-genome amplification... |
| create.timepoint.parser | Generate a closure function to parse timepoint labels from... |
| env.features | Env Feature Annotation |
| export.fasta.swarmset | Output fasta-formatted full-length sequence text for all... |
| export.swarmset | Output full-length sequence text for all selected sequences... |
| is.protein | verify that the input alignment consists of amino acids,... |
| lassie | lassie: Tools to select sequences that represent variation in... |
| make.timepoint.logos | Render a logo plot of concatamer forms of clones in... |
| plot.swarmset | Render a logo plot of concatamer forms of clones in... |
| plot.swarmtools | Plot a cumulative distribution function of number of sites... |
| pngs2o | Given amino acid sequence/s in one of several formats,... |
| prep.aln | Prepare input data for analysis after defining refseq,... |
| print.swarmset | List concatamers of selected sites for all working_swarm... |
| print.swarmtools | Print a table of the selected sites. |
| read.alignment.file | Read a fasta-formatted alignment file |
| report.variant.frequencies | Summarize and plot the frequency dynamics per site. |
| resample.swarmset | Randomly sample as many sequences as are in the given working... |
| set.alignment | Defines alignment file but does not read it. After setting... |
| set.alignment.file | Defines alignment file but does not read it, then call... |
| set.tf | Accessor method to update tf-derived variables (tf_loss,... |
| set.tf.loss.cutoff | Define the threshold value, above which sites are considered... |
| set.tp.parser | Update parser function, which extracts timepoint labels from... |
| summary.swarmset | List names of sequences in working_swarm of swarmset. |
| summary.swarmtools | Summarize selected sites. |
| swarmset | Select sequences to represent mutations in selected sites. |
| swarmtools | Identify sites under putative immune selection. |
| tabulate.swarmset | List concatamers of selected sites for all working_swarm... |
| vgrepl | Compare a vector of patterns with an input string |
