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

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

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