| ABBREV_AA | Amino acid abbreviation translations | 
| AbundanceCurve | S4 class defining a clonal abundance curve | 
| AbundanceCurve-class | S4 class defining a clonal abundance curve | 
| AbundanceCurve-method | S4 class defining a clonal abundance curve | 
| alakazam | The alakazam package | 
| aliphatic | Calculates the aliphatic index of amino acid sequences | 
| alphaDiversity | Calculate clonal alpha diversity | 
| aminoAcidProperties | Calculates amino acid chemical properties for sequence data | 
| baseTheme | Standard ggplot settings | 
| 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. | 
| checkColumns | Check data.frame for valid columns and issue message if invalid | 
| collapseDuplicates | Remove duplicate DNA sequences and combine annotations | 
| combineIgphyml | Combine IgPhyML object parameters into a dataframe | 
| countClones | Tabulates clones sizes | 
| countGenes | Tabulates V(D)J allele, gene or family usage. | 
| countPatterns | Count sequence patterns | 
| cpuCount | Available CPU cores | 
| DEFAULT_COLORS | Default colors | 
| DiversityCurve | S4 class defining a diversity curve | 
| DiversityCurve-class | S4 class defining a diversity curve | 
| DiversityCurve-method | S4 class defining a diversity curve | 
| DNA_COLORS | Default colors | 
| DNA_IUPAC | IUPAC ambiguous characters | 
| 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 | 
| Example10x | Small example 10x Genomics Ig V(D)J sequences from CD19+ B cells isolated from PBMCs of a healthy human donor. Down-sampled from data provided by 10x Genomics under a Creative Commons Attribute license, and processed with their Cell Ranger pipeline. | 
| ExampleDb | Example AIRR database | 
| ExampleDbChangeo | 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 | 
| getChain | 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 | 
| getLocus | 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 | 
| getPositionQuality | Get a data.frame with sequencing qualities per position | 
| getSegment | Get Ig segment allele, gene and family names | 
| graphToPhylo | Convert a tree in igraph 'graph' format to ape 'phylo' format. | 
| gravy | Calculates the hydrophobicity of amino acid sequences | 
| gridPlot | Plot multiple ggplot objects | 
| groupGenes | Group sequences by gene assignment | 
| 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 | 
| junctionAlignment | Calculate junction region alignment properties | 
| makeChangeoClone | Generate a ChangeoClone object for lineage construction | 
| makeTempDir | Create a temporary folder | 
| maskPositionsByQuality | Mask sequence positions with low quality | 
| 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 | 
| nonsquareDist | Calculate pairwise distances between sequences | 
| padSeqEnds | Pads ragged ends of aligned DNA sequences | 
| pairwiseDist | Calculate pairwise distances between sequences | 
| pairwiseEqual | Calculate pairwise equivalence between sequences | 
| permuteLabels | Permute the node labels of a tree | 
| phyloToGraph | Convert a tree in ape 'phylo' format to igraph 'graph' format. | 
| plot-method | S4 class defining a clonal abundance curve | 
| plot-method | S4 class defining a diversity curve | 
| plot-method | S4 class defining edge significance | 
| plot-method | S4 class defining edge significance | 
| plotAbundanceCurve | Plots a clonal abundance distribution | 
| plotDiversityCurve | Plot the results of alphaDiversity | 
| plotDiversityTest | Plot the results of diversity testing | 
| 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 a clonal abundance curve | 
| print-method | S4 class defining a diversity curve | 
| print-method | S4 class defining edge significance | 
| print-method | S4 class defining edge significance | 
| progressBar | Standard progress bar | 
| rarefyDiversity | Generate a clonal diversity index curve | 
| readChangeoDb | Read a Change-O tab-delimited database file | 
| readFastqDb | Load sequencing quality scores from a FASTQ file | 
| readIgphyml | Read in output from IgPhyML | 
| seqDist | Calculate distance between two sequences | 
| seqEqual | Test DNA sequences for equality. | 
| SingleDb | Single sequence AIRR database | 
| 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 |