alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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Provides immunoglobulin (Ig) sequence lineage reconstruction, diversity profiling, and amino acid property analysis. Also provides core functionality for other tools in the Change-O suite.

Author
Jason Vander Heiden [aut, cre], Namita Gupta [aut], Susanna Marquez [ctb], Daniel Gadala-Maria [ctb], Roy Jiang [ctb], Steven Kleinstein [aut, cph]
Date of publication
2016-08-06 00:19:53
Maintainer
Jason Vander Heiden <jason.vanderheiden@yale.edu>
License
CC BY-NC-SA 4.0
Version
0.2.5
URLs

View on CRAN

Man pages

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-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-class
S4 class defining diversity curve
DiversityTest-class
S4 class defining diversity significance
EdgeTest-class
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
getDNAMatrix
Build a DNA distance matrix
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
IMGT_REGIONS
IMGT V-segment regions
isValidAASeq
Validate amino acid sequences
IUPAC_CODES
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...
maskSeqGaps
Masks gap characters in DNA sequences
MRCATest-class
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
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
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...
testDiversity
Pairwise test of the diversity index
testEdges
Tests for parent-child annotation enchrichment in lineage...
testMRCA
Tests for MRCA annotation enrichment in lineage trees
translateDNA
Translate nucleotide sequences to amino acids
translateStrings
Translate a vector of strings
writeChangeoDb
Write a Change-O tab-delimited database file

Files in this package

alakazam
alakazam/inst
alakazam/inst/CITATION
alakazam/inst/doc
alakazam/inst/doc/Diversity-Vignette.Rmd
alakazam/inst/doc/AminoAcids-Vignette.Rmd
alakazam/inst/doc/Topology-Vignette.Rmd
alakazam/inst/doc/Topology-Vignette.pdf
alakazam/inst/doc/Lineage-Vignette.R
alakazam/inst/doc/AminoAcids-Vignette.R
alakazam/inst/doc/Lineage-Vignette.Rmd
alakazam/inst/doc/Diversity-Vignette.pdf
alakazam/inst/doc/Topology-Vignette.R
alakazam/inst/doc/Diversity-Vignette.R
alakazam/inst/doc/Lineage-Vignette.pdf
alakazam/inst/doc/AminoAcids-Vignette.pdf
alakazam/inst/markr
alakazam/inst/markr/build.R
alakazam/src
alakazam/src/RcppDistance.cpp
alakazam/src/RcppExports.cpp
alakazam/NAMESPACE
alakazam/NEWS.md
alakazam/data
alakazam/data/ExampleTrees.rda
alakazam/data/ExampleDb.rda
alakazam/R
alakazam/R/Data.R
alakazam/R/Core.R
alakazam/R/AminoAcids.R
alakazam/R/Gene.R
alakazam/R/Lineage.R
alakazam/R/sysdata.rda
alakazam/R/RcppExports.R
alakazam/R/Topology.R
alakazam/R/Sequence.R
alakazam/R/Alakazam.R
alakazam/R/Diversity.R
alakazam/R/Classes.R
alakazam/vignettes
alakazam/vignettes/Diversity-Vignette.Rmd
alakazam/vignettes/AminoAcids-Vignette.Rmd
alakazam/vignettes/Topology-Vignette.Rmd
alakazam/vignettes/Lineage-Vignette.Rmd
alakazam/README.md
alakazam/MD5
alakazam/build
alakazam/build/vignette.rds
alakazam/DESCRIPTION
alakazam/man
alakazam/man/testEdges.Rd
alakazam/man/makeChangeoClone.Rd
alakazam/man/aminoAcidProperties.Rd
alakazam/man/buildPhylipLineage.Rd
alakazam/man/MRCATest-class.Rd
alakazam/man/pairwiseEqual.Rd
alakazam/man/pairwiseDist.Rd
alakazam/man/alakazam.Rd
alakazam/man/aliphatic.Rd
alakazam/man/writeChangeoDb.Rd
alakazam/man/plotAbundance.Rd
alakazam/man/plotSubtrees.Rd
alakazam/man/charge.Rd
alakazam/man/bulk.Rd
alakazam/man/getMRCA.Rd
alakazam/man/ExampleDb.Rd
alakazam/man/DEFAULT_COLORS.Rd
alakazam/man/tableEdges.Rd
alakazam/man/polar.Rd
alakazam/man/sortGenes.Rd
alakazam/man/DiversityCurve-class.Rd
alakazam/man/testMRCA.Rd
alakazam/man/EdgeTest-class.Rd
alakazam/man/translateStrings.Rd
alakazam/man/estimateAbundance.Rd
alakazam/man/maskSeqEnds.Rd
alakazam/man/DiversityTest-class.Rd
alakazam/man/collapseDuplicates.Rd
alakazam/man/getSegment.Rd
alakazam/man/permuteLabels.Rd
alakazam/man/IMGT_REGIONS.Rd
alakazam/man/ABBREV_AA.Rd
alakazam/man/countPatterns.Rd
alakazam/man/plotDiversityCurve.Rd
alakazam/man/calcDiversity.Rd
alakazam/man/maskSeqGaps.Rd
alakazam/man/IUPAC_CODES.Rd
alakazam/man/ChangeoClone-class.Rd
alakazam/man/seqDist.Rd
alakazam/man/stoufferMeta.Rd
alakazam/man/testDiversity.Rd
alakazam/man/plotMRCATest.Rd
alakazam/man/countGenes.Rd
alakazam/man/translateDNA.Rd
alakazam/man/makeTempDir.Rd
alakazam/man/gridPlot.Rd
alakazam/man/getDNAMatrix.Rd
alakazam/man/readChangeoDb.Rd
alakazam/man/seqEqual.Rd
alakazam/man/countClones.Rd
alakazam/man/calcCoverage.Rd
alakazam/man/ExampleTrees.Rd
alakazam/man/getAAMatrix.Rd
alakazam/man/rarefyDiversity.Rd
alakazam/man/gravy.Rd
alakazam/man/getPathLengths.Rd
alakazam/man/extractVRegion.Rd
alakazam/man/summarizeSubtrees.Rd
alakazam/man/isValidAASeq.Rd
alakazam/man/plotEdgeTest.Rd