alakazam package - RDocumentation

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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:

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.
Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
Performing clonal abundance and diversity analysis on lymphocyte repertoires.
Performing lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
Performing physicochemical property analyses of lymphocyte receptor sequences.

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Version

Install

install.packages('alakazam')

Monthly Downloads

1,267

Version

1.4.0

License

AGPL-3

Maintainer

Susanna Marquez

Last Published

September 25th, 2025

Functions in alakazam (1.4.0)

S4 class defining edge significance

Single sequence AIRR database

Calculates the average bulkiness of amino acid sequences

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

collapseDuplicates

Remove duplicate DNA sequences and combine annotations

Calculate the diversity index

Tabulates clones sizes

Calculates the net charge of amino acid sequences.

Combine IgPhyML object parameters into a dataframe

Tabulates V(D)J allele, gene or family usage within each locus.

buildPhylipLineage

Infer an Ig lineage using PHYLIP

Calculate sample coverage

getPositionQuality

Get a data.frame with sequencing qualities per position

estimateAbundance

Estimates the complete clonal relative abundance distribution

Count sequence patterns

Retrieve the first non-root node of a lineage tree

Build an AA distance matrix

Available CPU cores

Calculate path lengths from the tree root

Extracts FWRs and CDRs from IMGT-gapped sequences

Get Ig segment allele, gene and family names

Build a DNA distance matrix

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

Masks ragged leading and trailing edges of aligned DNA sequences

Create a temporary folder

Validate amino acid sequences

maskPositionsByQuality

Mask sequence positions with low quality

Group sequences by gene assignment

junctionAlignment

Calculate junction region alignment properties

Calculates the hydrophobicity of amino acid sequences

makeChangeoClone

Generate a ChangeoClone object for lineage construction

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

plotAbundanceCurve

Plot a clonal abundance distribution

Calculate pairwise equivalence between sequences

Permute the node labels of a tree

plotDiversityTest

Plot the results of diversity testing

Calculate pairwise distances between sequences

plotDiversityCurve

Plot the results of alphaDiversity

Pads ragged ends of aligned DNA sequences

Calculate pairwise distances between sequences

Plot multiple ggplot objects

Masks gap characters in DNA sequences

rarefyDiversity

Generate a clonal diversity index curve

Standard progress bar

Load sequencing quality scores from a FASTQ file

Calculates the average polarity of amino acid sequences

Calculate distance between two sequences

Read in output from IgPhyML

Read a Change-O tab-delimited database file

Plot the results of an edge permutation test

Plot the results of a founder permutation test

Plots subtree statistics for multiple trees

Tabulate the number of edges between annotations within a lineage tree

translateStrings

Translate a vector of strings

Tests for MRCA annotation enrichment in lineage trees

Tests for parent-child annotation enrichment in lineage trees

Sort V(D)J genes

Pairwise test of the diversity index

Test DNA sequences for equality.

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

summarizeSubtrees

Generate subtree summary statistics for a tree

Translate nucleotide sequences to amino acids

Write a Change-O tab-delimited database file

AbundanceCurve-class

S4 class defining a clonal abundance curve

ChangeoClone-class

S4 class defining a clone

Amino acid abbreviation translations

S4 class defining edge significance

DiversityCurve-class

S4 class defining a diversity curve

Standard ggplot settings

Calculate clonal alpha diversity

Calculates the aliphatic index of amino acid sequences

aminoAcidProperties

Calculates amino acid chemical properties for sequence data

The Alakazam package

IMGT V-segment regions

ExampleDbChangeo

Example Change-O database

alakazam-package

alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Example AIRR database

Example Ig lineage trees

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.

IUPAC ambiguous characters