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Alakazam

Alakazam is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of tools to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties, with a focus on high-throughput immunoglobulin (Ig) sequencing.

Alakazam serves five main purposes:

  1. Providing core functionality for other R packages in the Immcantation framework. This includes common tasks such as file I/O, basic DNA sequence manipulation, and interacting with V(D)J segment and gene annotations.
  2. Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
  3. Performing clonal abundance and diversity analysis on lymphocyte repertoires.
  4. Performing lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
  5. Performing physicochemical property analyses of lymphocyte receptor sequences.

Contact

For help and questions, please contact the Immcantation Group or use the issue tracker.

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Version

Install

install.packages('alakazam')

Monthly Downloads

1,422

Version

1.2.1

License

AGPL-3

Maintainer

Jason Vander Heiden

Last Published

September 20th, 2022

Functions in alakazam (1.2.1)

MRCATest-class

S4 class defining edge significance
Example10x

Small example 10x Genomics Ig V(D)J sequences from CD19+ B cells isolated from PBMCs of a healthy human donor. Down-sampled from data provided by 10x Genomics under a Creative Commons Attribute license, and processed with their Cell Ranger pipeline.
SingleDb

Single sequence AIRR database
buildPhylipLineage

Infer an Ig lineage using PHYLIP
baseTheme

Standard ggplot settings
ExampleDbChangeo

Example Change-O database
ExampleTrees

Example Ig lineage trees
IMGT_REGIONS

IMGT V-segment regions
ExampleDb

Example AIRR database
collapseDuplicates

Remove duplicate DNA sequences and combine annotations
checkColumns

Check data.frame for valid columns and issue message if invalid
alphaDiversity

Calculate clonal alpha diversity
AbundanceCurve-class

S4 class defining a clonal abundance curve
countPatterns

Count sequence patterns
ABBREV_AA

Amino acid abbreviation translations
getPathLengths

Calculate path lengths from the tree root
aminoAcidProperties

Calculates amino acid chemical properties for sequence data
getPositionQuality

Get a data.frame with sequencing qualities per position
countGenes

Tabulates V(D)J allele, gene or family usage.
IUPAC_CODES

IUPAC ambiguous characters
countClones

Tabulates clones sizes
combineIgphyml

Combine IgPhyML object parameters into a dataframe
cpuCount

Available CPU cores
estimateAbundance

Estimates the complete clonal relative abundance distribution
extractVRegion

Extracts FWRs and CDRs from IMGT-gapped sequences
graphToPhylo

Convert a tree in igraph graph format to ape phylo format.
getSegment

Get Ig segment allele, gene and family names
calcDiversity

Calculate the diversity index
aliphatic

Calculates the aliphatic index of amino acid sequences
junctionAlignment

Calculate junction region alignment properties
getMRCA

Retrieve the first non-root node of a lineage tree
getDNAMatrix

Build a DNA distance matrix
charge

Calculates the net charge of amino acid sequences.
alakazam

The alakazam package
plotDiversityTest

Plot the results of diversity testing
plotEdgeTest

Plot the results of an edge permutation test
plotAbundanceCurve

Plots a clonal abundance distribution
makeChangeoClone

Generate a ChangeoClone object for lineage construction
plotDiversityCurve

Plot the results of alphaDiversity
maskSeqGaps

Masks gap characters in DNA sequences
readIgphyml

Read in output from IgPhyML
phyloToGraph

Convert a tree in ape phylo format to igraph graph format.
readFastqDb

Load sequencing quality scores from a FASTQ file
maskSeqEnds

Masks ragged leading and trailing edges of aligned DNA sequences
polar

Calculates the average polarity of amino acid sequences
permuteLabels

Permute the node labels of a tree
progressBar

Standard progress bar
gravy

Calculates the hydrophobicity of amino acid sequences
plotMRCATest

Plot the results of a founder permutation test
nonsquareDist

Calculate pairwise distances between sequences
gridPlot

Plot multiple ggplot objects
plotSubtrees

Plots subtree statistics for multiple trees
padSeqEnds

Pads ragged ends of aligned DNA sequences
bulk

Calculates the average bulkiness of amino acid sequences
pairwiseDist

Calculate pairwise distances between sequences
groupGenes

Group sequences by gene assignment
translateStrings

Translate a vector of strings
isValidAASeq

Validate amino acid sequences
calcCoverage

Calculate sample coverage
rarefyDiversity

Generate a clonal diversity index curve
pairwiseEqual

Calculate pairwise equivalence between sequences
testDiversity

Pairwise test of the diversity index
sortGenes

Sort V(D)J genes
stoufferMeta

Weighted meta-analysis of p-values via Stouffer's method
testEdges

Tests for parent-child annotation enchrichment in lineage trees
tableEdges

Tabulate the number of edges between annotations within a lineage tree
readChangeoDb

Read a Change-O tab-delimited database file
writeChangeoDb

Write a Change-O tab-delimited database file
seqDist

Calculate distance between two sequences
translateDNA

Translate nucleotide sequences to amino acids
makeTempDir

Create a temporary folder
seqEqual

Test DNA sequences for equality.
getAAMatrix

Build an AA distance matrix
maskPositionsByQuality

Mask sequence positions with low quality
testMRCA

Tests for MRCA annotation enrichment in lineage trees
summarizeSubtrees

Generate subtree summary statistics for a tree
ChangeoClone-class

S4 class defining a clone
DEFAULT_COLORS

Default colors
EdgeTest-class

S4 class defining edge significance
DiversityCurve-class

S4 class defining a diversity curve