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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

1.3.0

License

AGPL-3

Maintainer

Susanna Marquez

Last Published

September 30th, 2023

Functions in alakazam (1.3.0)

MRCATest-class

S4 class defining edge significance
alphaDiversity

Calculate clonal alpha diversity
SingleDb

Single sequence AIRR database
IMGT_REGIONS

IMGT V-segment regions
baseTheme

Standard ggplot settings
aliphatic

Calculates the aliphatic index of amino acid sequences
aminoAcidProperties

Calculates amino acid chemical properties for sequence data
alakazam

The Alakazam package
alakazam-package

alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis
IUPAC_CODES

IUPAC ambiguous characters
checkColumns

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

Infer an Ig lineage using PHYLIP
bulk

Calculates the average bulkiness of amino acid sequences
charge

Calculates the net charge of amino acid sequences.
combineIgphyml

Combine IgPhyML object parameters into a dataframe
collapseDuplicates

Remove duplicate DNA sequences and combine annotations
countGenes

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

Calculate sample coverage
calcDiversity

Calculate the diversity index
countClones

Tabulates clones sizes
countPatterns

Count sequence patterns
getSegment

Get Ig segment allele, gene and family names
getAAMatrix

Build an AA distance matrix
getDNAMatrix

Build a DNA distance matrix
getMRCA

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

Get a data.frame with sequencing qualities per position
cpuCount

Available CPU cores
extractVRegion

Extracts FWRs and CDRs from IMGT-gapped sequences
getPathLengths

Calculate path lengths from the tree root
estimateAbundance

Estimates the complete clonal relative abundance distribution
maskPositionsByQuality

Mask sequence positions with low quality
graphToPhylo

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

Plot multiple ggplot objects
maskSeqEnds

Masks ragged leading and trailing edges of aligned DNA sequences
groupGenes

Group sequences by gene assignment
junctionAlignment

Calculate junction region alignment properties
isValidAASeq

Validate amino acid sequences
makeTempDir

Create a temporary folder
makeChangeoClone

Generate a ChangeoClone object for lineage construction
pairwiseEqual

Calculate pairwise equivalence between sequences
pairwiseDist

Calculate pairwise distances between sequences
plotDiversityCurve

Plot the results of alphaDiversity
gravy

Calculates the hydrophobicity of amino acid sequences
padSeqEnds

Pads ragged ends of aligned DNA sequences
plotDiversityTest

Plot the results of diversity testing
maskSeqGaps

Masks gap characters in DNA sequences
phyloToGraph

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

Plot a clonal abundance distribution
permuteLabels

Permute the node labels of a tree
nonsquareDist

Calculate pairwise distances between sequences
readChangeoDb

Read a Change-O tab-delimited database file
progressBar

Standard progress bar
readFastqDb

Load sequencing quality scores from a FASTQ file
rarefyDiversity

Generate a clonal diversity index curve
readIgphyml

Read in output from IgPhyML
plotEdgeTest

Plot the results of an edge permutation test
seqDist

Calculate distance between two sequences
plotSubtrees

Plots subtree statistics for multiple trees
polar

Calculates the average polarity of amino acid sequences
plotMRCATest

Plot the results of a founder permutation test
translateDNA

Translate nucleotide sequences to amino acids
stoufferMeta

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

Pairwise test of the diversity index
sortGenes

Sort V(D)J genes
translateStrings

Translate a vector of strings
testMRCA

Tests for MRCA annotation enrichment in lineage trees
tableEdges

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

Test DNA sequences for equality.
testEdges

Tests for parent-child annotation enrichment in lineage trees
summarizeSubtrees

Generate subtree summary statistics for a tree
writeChangeoDb

Write a Change-O tab-delimited database file
ABBREV_AA

Amino acid abbreviation translations
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.
ChangeoClone-class

S4 class defining a clone
DiversityCurve-class

S4 class defining a diversity curve
EdgeTest-class

S4 class defining edge significance
AbundanceCurve-class

S4 class defining a clonal abundance curve
ExampleTrees

Example Ig lineage trees
DEFAULT_COLORS

Default colors
ExampleDb

Example AIRR database
ExampleDbChangeo

Example Change-O database