R: The alakazam package

alakazam {alakazam} | R Documentation

## The alakazam package

### Description

`alakazam` in a member of the Change-O suite of tools and serves five main purposes:

- Providing core functionality for other R packages in the Change-O suite. 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 tool suite.

- Performing lineage reconstruction on clonal populations of immunoglobulin (Ig) sequences.

- Performing clonal abundance and diversity analysis on lymphocyte repertoires.

- Performing physicochemical property analyses of lymphocyte receptor sequences.

For additional details regarding the use of the `alakazam` package see the vignettes:
`browseVignettes("alakazam")`

### File I/O

- readChangeoDb: Input Change-O style files.

- writeChangeoDb: Output Change-O style files.

### Sequence cleaning

- maskSeqEnds: Mask ragged ends.

- maskSeqGaps: Mask gap characters.

- collapseDuplicates: Remove duplicate sequences.

### Lineage reconstruction

- makeChangeoClone: Clean sequences for lineage reconstruction.

- buildPhylipLineage: Perform lineage reconstruction of Ig sequences.

### Lineage topology analysis

- tableEdges: Tabulate annotation relationships over edges.

- testEdges: Significance testing of annotation edges.

- testMRCA: Significance testing of MRCA annotations.

- summarizeSubtrees: Various summary statistics for subtrees.

- plotSubtrees: Plot distributions of summary statistics for a population of trees.

### Diversity analysis

- countClones: Calculate clonal abundance.

- estimateAbundance: Bootstrap clonal abundance curves.

- alphaDiversity: Generate clonal alpha diversity curves.

- plotAbundanceCurve: Plot clone size distribution as a rank-abundance

- plotDiversityCurve: Plot clonal diversity curves.

- plotDiversityTest: Plot testing at given diversity hill indicex.

### Ig and TCR sequence annotation

- countGenes: Calculate Ig and TCR allele, gene and family usage.

- extractVRegion: Extract CDRs and FWRs sub-sequences.

- getAllele: Get V(D)J allele names.

- getGene: Get V(D)J gene names.

- getFamily: Get V(D)J family names.

### Sequence distance calculation

- seqDist: Calculate Hamming distance between two sequences.

- seqEqual: Test two sequences for equivalence.

- pairwiseDist: Calculate a matrix of pairwise Hamming distances for a set of sequences.

- pairwiseEqual: Calculate a logical matrix of pairwise equivalence for a set of sequences.

### Amino acid propertes

- translateDNA: Translate DNA sequences to amino acid sequences.

- aminoAcidProperties: Calculate various physicochemical properties of amino acid sequences.

- countPatterns: Count patterns in sequences.

### General data manipulation

- translateStrings: Perform multiple string replacement operations.

### References

1. Vander Heiden JA, Yaari G, et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014 30(13):1930-2.

2. Stern JNH, Yaari G, Vander Heiden JA, et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014 6(248):248ra107.

3. Wu Y-CB, et al. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. J Allergy Clin Immunol. 2014 134(3):604-12.

4. Gupta NT, Vander Heiden JA, et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. 2015 Oct 15;31(20):3356-8.

[Package alakazam version 0.3.0 Index]