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| aclust | aclust |
| AMPSequences | Antimicrobial peptide sequences |
| AMPSequences.response | Antimicrobial peptide sequence responses |
| BIC | Bayesian Information Content |
| BIC-method | Class "MotifModel" |
| BIC-method | Class "MotifModelSet" |
| blosum50 | BLOSUM 50 substitution matrix |
| blosum62 | BLOSUM 62 substitution matrix |
| blosum90 | BLOSUM 90 substitution matrix |
| changeClusterFormat | Change cluster format |
| classify | classify |
| classify-method | Class "MotifModelSet" |
| default.MetricParams | Default parameters for calculating sequence-sequence distances |
| defaultBaseMatrix | defaultBaseMatrix |
| Descriptors | Class "Descriptors" |
| descriptors | Class "Descriptors" |
| Descriptors-class | Class "Descriptors" |
| dist-method | Class "Sequences" |
| logLik-method | Class "MotifModel" |
| logLik-method | Class "MotifModelSet" |
| MetricParams | Class "MetricParams" |
| MetricParams-class | Class "MetricParams" |
| MotifModel | Class "MotifModel" |
| motifModel | Class "MotifModel" |
| MotifModel-class | Class "MotifModel" |
| MotifModelSet | Class "MotifModelSet" |
| motifModelSet | Class "MotifModelSet" |
| MotifModelSet-class | Class "MotifModelSet" |
| motifString | Class "MotifModel" |
| motifString-method | Class "MotifModel" |
| plot-method | Class "Descriptors" |
| plot-method | Class "MotifModel" |
| plot-method | Class "MotifModelSet" |
| plot-method | Class "Sequences" |
| plotFits | Class "MotifModel" |
| plotFits-method | Class "MotifModel" |
| plotPositions | Class "MotifModel" |
| plotPositions-method | Class "MotifModel" |
| plotStartingPosition | Class "MotifModel" |
| plotStartingPosition-method | Class "MotifModel" |
| predict-method | Class "MotifModel" |
| predict-method | Class "MotifModelSet" |
| print-method | Class "MotifModel" |
| rbind-method | Class "Sequences" |
| read.fasta | Read in sequences in FASTA format |
| read.sequences | Read sequence file |
| residuals-method | Class "MotifModel" |
| residuals-method | Class "MotifModelSet" |
| Sequences | Class "Sequences" |
| Sequences-class | Class "Sequences" |
| SHP2Sequences | SHP-2_N-SH2 peptide sequences |
| simpleDescriptors | Function "simpleDescriptors" |
| TULASequences | TULA-2_Post peptide sequences |
| write.fasta | Write out the sequences as a FASTA file |
| write.sequences | Write out the sequences as a sequence file |
| [-method | Class "Sequences" |