![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| alakazam-package | The alakazam package |
| ABBREV_AA | Amino acid abbreviation translations |
| alakazam | The alakazam package |
| aliphatic | Calculates the aliphatic index of amino acid sequences |
| aminoAcidProperties | Calculates amino acid chemical properties for sequence data |
| buildPhylipLineage | Infer an Ig lineage using PHYLIP |
| bulk | Calculates the average bulkiness of amino acid sequences |
| calcCoverage | Calculate sample coverage |
| calcDiversity | Calculate the diversity index |
| ChangeoClone | S4 class defining a clone |
| ChangeoClone-class | S4 class defining a clone |
| charge | Calculates the net charge of amino acid sequences. |
| collapseDuplicates | Remove duplicate DNA sequences and combine annotations |
| countClones | Tabulates clones sizes |
| countGenes | Tabulates V(D)J allele, gene or family usage. |
| countPatterns | Count sequence patterns |
| DEFAULT_COLORS | Default colors |
| DiversityCurve | S4 class defining diversity curve |
| DiversityCurve-class | S4 class defining diversity curve |
| DiversityCurve-method | S4 class defining diversity curve |
| DiversityTest | S4 class defining diversity significance |
| DiversityTest-class | S4 class defining diversity significance |
| DiversityTest-method | S4 class defining diversity significance |
| DNA_COLORS | Default colors |
| EdgeTest | S4 class defining edge significance |
| EdgeTest-class | S4 class defining edge significance |
| EdgeTest-method | S4 class defining edge significance |
| estimateAbundance | Estimates the complete clonal relative abundance distribution |
| ExampleDb | Example Change-O database |
| ExampleTrees | Example Ig lineage trees |
| extractVRegion | Extracts FWRs and CDRs from IMGT-gapped sequences |
| getAAMatrix | Build an AA distance matrix |
| getAllele | Get Ig segment allele, gene and family names |
| getDNAMatrix | Build a DNA distance matrix |
| getFamily | Get Ig segment allele, gene and family names |
| getGene | Get Ig segment allele, gene and family names |
| getMRCA | Retrieve the first non-root node of a lineage tree |
| getPathLengths | Calculate path lengths from the tree root |
| getSegment | Get Ig segment allele, gene and family names |
| gravy | Calculates the hydrophobicity of amino acid sequences |
| gridPlot | Plot multiple ggplot objects |
| IG_COLORS | Default colors |
| IMGT_REGIONS | IMGT V-segment regions |
| isValidAASeq | Validate amino acid sequences |
| IUPAC_AA | IUPAC ambiguous characters |
| IUPAC_CODES | IUPAC ambiguous characters |
| IUPAC_DNA | IUPAC ambiguous characters |
| makeChangeoClone | Generate a ChangeoClone object for lineage construction |
| makeTempDir | Create a temporary folder |
| maskSeqEnds | Masks ragged leading and trailing edges of aligned DNA sequences |
| maskSeqGaps | Masks gap characters in DNA sequences |
| MRCATest | S4 class defining edge significance |
| MRCATest-class | S4 class defining edge significance |
| MRCATest-method | S4 class defining edge significance |
| pairwiseDist | Calculate pairwise distances between sequences |
| pairwiseEqual | Calculate pairwise equivalence between sequences |
| permuteLabels | Permute the node labels of a tree |
| plot-method | S4 class defining diversity curve |
| plot-method | S4 class defining edge significance |
| plot-method | S4 class defining edge significance |
| plotAbundance | Plots a clonal abundance distribution |
| plotDiversityCurve | Plot the results of rarefyDiversity |
| plotEdgeTest | Plot the results of an edge permutation test |
| plotMRCATest | Plot the results of a founder permutation test |
| plotSubtrees | Plots subtree statistics for multiple trees |
| polar | Calculates the average polarity of amino acid sequences |
| print-method | S4 class defining diversity curve |
| print-method | S4 class defining diversity significance |
| print-method | S4 class defining edge significance |
| print-method | S4 class defining edge significance |
| rarefyDiversity | Generate a clonal diversity index curve |
| readChangeoDb | Read a Change-O tab-delimited database file |
| seqDist | Calculate distance between two sequences |
| seqEqual | Test DNA sequences for equality. |
| sortGenes | Sort V(D)J genes |
| stoufferMeta | Weighted meta-analysis of p-values via Stouffer's method |
| summarizeSubtrees | Generate subtree summary statistics for a tree |
| tableEdges | Tabulate the number of edges between annotations within a lineage tree |
| testDiversity | Pairwise test of the diversity index |
| testEdges | Tests for parent-child annotation enchrichment in lineage trees |
| testMRCA | Tests for MRCA annotation enrichment in lineage trees |
| translateDNA | Translate nucleotide sequences to amino acids |
| translateStrings | Translate a vector of strings |
| TR_COLORS | Default colors |
| writeChangeoDb | Write a Change-O tab-delimited database file |