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 |
DiversityTest | S4 class defining diversity significance |
DiversityTest-class | S4 class defining diversity significance |
DNA_COLORS | Default colors |
estimateAbundance | Estimates the complete clonal relative abundance distribution |
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 |
getSegment | Get Ig segment allele, gene and family names |
getSeqDistance | Calculate distance between two sequences |
getSeqMatrix | Calculate pairwise distances between sequences |
gravy | Calculates the hydrophobicity of amino acid sequences |
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 |
multiggplot | Plot multiple ggplot objects |
plotAbundance | Plots a clonal abundance distribution |
plotDiversityCurve | Plot the results of rarefyDiversity |
polar | Calculates the average polarity of amino acid sequences |
print-method | S4 class defining diversity curve |
print-method | S4 class defining diversity significance |
rarefyDiversity | Generate a clonal diversity index curve |
readChangeoDb | Read a Change-O tab-delimited database file |
stoufferMeta | Weighted meta-analysis of p-values via Stouffer's method |
testDiversity | Pairwise test of the diversity index |
testSeqEqual | Test DNA sequences for equality. |
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 |