Man pages for phraber/lassie
Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment

aa.colColor Look-up-Table
CH505Within-host longitudinal Env single-genome amplification...
create.timepoint.parserGenerate a closure function to parse timepoint labels from...
env.featuresEnv Feature Annotation
export.fasta.swarmsetOutput fasta-formatted full-length sequence text for all...
export.swarmsetOutput full-length sequence text for all selected sequences...
is.proteinverify that the input alignment consists of amino acids,...
lassielassie: Tools to select sequences that represent variation in...
make.timepoint.logosRender a logo plot of concatamer forms of clones in...
plot.swarmsetRender a logo plot of concatamer forms of clones in...
plot.swarmtoolsPlot a cumulative distribution function of number of sites...
pngs2oGiven amino acid sequence/s in one of several formats,...
prep.alnPrepare input data for analysis after defining refseq,...
print.swarmsetList concatamers of selected sites for all working_swarm...
print.swarmtoolsPrint a table of the selected sites.
read.alignment.fileRead a fasta-formatted alignment file
report.variant.frequenciesSummarize and plot the frequency dynamics per site.
resample.swarmsetRandomly sample as many sequences as are in the given working...
set.alignmentDefines alignment file but does not read it. After setting...
set.alignment.fileDefines alignment file but does not read it, then call...
set.tfAccessor method to update tf-derived variables (tf_loss,...
set.tf.loss.cutoffDefine the threshold value, above which sites are considered...
set.tp.parserUpdate parser function, which extracts timepoint labels from...
summary.swarmsetList names of sequences in working_swarm of swarmset.
summary.swarmtoolsSummarize selected sites.
swarmsetSelect sequences to represent mutations in selected sites.
swarmtoolsIdentify sites under putative immune selection.
tabulate.swarmsetList concatamers of selected sites for all working_swarm...
vgreplCompare a vector of patterns with an input string
phraber/lassie documentation built on Oct. 22, 2018, 11:29 p.m.