alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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.

AuthorJason Vander Heiden [aut, cre], Namita Gupta [aut], Susanna Marquez [ctb], Daniel Gadala-Maria [ctb], Roy Jiang [ctb], Steven Kleinstein [aut, cph]
Date of publication2016-08-06 00:19:53
MaintainerJason Vander Heiden <jason.vanderheiden@yale.edu>
LicenseCC BY-NC-SA 4.0
Version0.2.5
http://alakazam.readthedocs.org

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

Functions

ABBREV_AA Man page
alakazam Man page
alakazam-package Man page
aliphatic Man page
aminoAcidProperties Man page
buildPhylipLineage Man page
bulk Man page
calcCoverage Man page
calcDiversity Man page
ChangeoClone Man page
ChangeoClone-class Man page
charge Man page
collapseDuplicates Man page
countClones Man page
countGenes Man page
countPatterns Man page
DEFAULT_COLORS Man page
DiversityCurve Man page
DiversityCurve-class Man page
DiversityCurve-method Man page
DiversityTest Man page
DiversityTest-class Man page
DiversityTest-method Man page
DNA_COLORS Man page
EdgeTest Man page
EdgeTest-class Man page
EdgeTest-method Man page
estimateAbundance Man page
ExampleDb Man page
ExampleTrees Man page
extractVRegion Man page
getAAMatrix Man page
getAllele Man page
getDNAMatrix Man page
getFamily Man page
getGene Man page
getMRCA Man page
getPathLengths Man page
getSegment Man page
gravy Man page
gridPlot Man page
IG_COLORS Man page
IMGT_REGIONS Man page
isValidAASeq Man page
IUPAC_AA Man page
IUPAC_CODES Man page
IUPAC_DNA Man page
makeChangeoClone Man page
makeTempDir Man page
maskSeqEnds Man page
maskSeqGaps Man page
MRCATest Man page
MRCATest-class Man page
MRCATest-method Man page
pairwiseDist Man page
pairwiseEqual Man page
permuteLabels Man page
plotAbundance Man page
plotDiversityCurve Man page
plot,DiversityCurve,missing-method Man page
plotEdgeTest Man page
plot,EdgeTest,missing-method Man page
plotMRCATest Man page
plot,MRCATest,missing-method Man page
plotSubtrees Man page
polar Man page
print,DiversityCurve-method Man page
print,DiversityTest-method Man page
print,EdgeTest-method Man page
print,MRCATest-method Man page
rarefyDiversity Man page
readChangeoDb Man page
seqDist Man page
seqEqual Man page
sortGenes Man page
stoufferMeta Man page
summarizeSubtrees Man page
tableEdges Man page
testDiversity Man page
testEdges Man page
testMRCA Man page
translateDNA Man page
translateStrings Man page
TR_COLORS Man page
writeChangeoDb Man page

Files

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

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