alakazam-package | The alakazam package |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
plot-method | S4 class defining a clonal abundance curve |
plot-method | S4 class defining a diversity curve |
plot-method | S4 class defining diversity significance |
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 rarefyDiversity |
plotDiversityTest | Plot the results of TestDiversity |
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 diversity significance |
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 |
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 |