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alakazam (version 0.2.2)
Immunoglobulin Clonal Lineage and Diversity Analysis
Description
Core functionality, lineage reconstruction, and diversity analysis, and amino acid property analysis components of the Change-O tool suite.
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Install
install.packages('alakazam')
Monthly Downloads
1,638
Version
0.2.2
License
CC BY-NC-SA 4.0
Maintainer
Jason Vander Heiden
Last Published
January 29th, 2016
Functions in alakazam (0.2.2)
Search functions
ExampleTrees
Example Ig lineage trees
charge
Calculates the net charge of amino acid sequences.
polar
Calculates the average polarity of amino acid sequences
DiversityTest-class
S4 class defining diversity significance
maskSeqEnds
Masks ragged leading and trailing edges of aligned DNA sequences
translateStrings
Translate a vector of strings
aminoAcidProperties
Calculates amino acid chemical properties for sequence data
testDiversity
Pairwise test of the diversity index
getDNAMatrix
Build a DNA distance matrix
maskSeqGaps
Masks gap characters in DNA sequences
IMGT_REGIONS
IMGT V-segment regions
readChangeoDb
Read a Change-O tab-delimited database file
makeTempDir
Create a temporary folder
multiggplot
Plot multiple ggplot objects
getSeqDistance
Calculate distance between two sequences
getAAMatrix
Build an AA distance matrix
countPatterns
Count sequence patterns
getSegment
Get Ig segment allele, gene and family names
countGenes
Tabulates V(D)J allele, gene or family usage.
plotAbundance
Plots a clonal abundance distribution
calcCoverage
Calculate sample coverage
plotDiversityCurve
Plot the results of rarefyDiversity
calcDiversity
Calculate the diversity index
rarefyDiversity
Generate a clonal diversity index curve
translateDNA
Translate nucleotide sequences to amino acids
DEFAULT_COLORS
Default colors
ChangeoClone-class
S4 class defining a clone
gravy
Calculates the hydrophobicity of amino acid sequences
makeChangeoClone
Generate a ChangeoClone object for lineage construction
isValidAASeq
Validate amino acid sequences
countClones
Tabulates clones sizes
extractVRegion
Extracts FWRs and CDRs from IMGT-gapped sequences
writeChangeoDb
Write a Change-O tab-delimited database file
estimateAbundance
Estimates the complete clonal relative abundance distribution
buildPhylipLineage
Infer an Ig lineage using PHYLIP
DiversityCurve-class
S4 class defining diversity curve
alakazam
The alakazam package
IUPAC_CODES
IUPAC ambiguous characters
ABBREV_AA
Amino acid abbreviation translations
collapseDuplicates
Remove duplicate DNA sequences and combine annotations
testSeqEqual
Test DNA sequences for equality.
getSeqMatrix
Calculate pairwise distances between sequences
bulk
Calculates the average bulkiness of amino acid sequences
stoufferMeta
Weighted meta-analysis of p-values via Stouffer's method
aliphatic
Calculates the aliphatic index of amino acid sequences