alakazam | R Documentation |
alakazam
in a member of the Immcantation framework of tools and serves five main
purposes:
Providing core functionality for other R packages in Immcantation. 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 immunoglobulin (Ig) sequences.
Performing physicochemical property analyses of lymphocyte receptor sequences.
For additional details regarding the use of the alakazam
package see the
vignettes:
browseVignettes("alakazam")
readChangeoDb: Input Change-O style files.
writeChangeoDb: Output Change-O style files.
maskSeqEnds: Mask ragged ends.
maskSeqGaps: Mask gap characters.
collapseDuplicates: Remove duplicate sequences.
makeChangeoClone: Clean sequences for lineage reconstruction.
buildPhylipLineage: Perform lineage reconstruction of Ig sequences.
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.
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.
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.
junctionAlignment: Junction alignment properties
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.
translateDNA: Translate DNA sequences to amino acid sequences.
aminoAcidProperties: Calculate various physicochemical properties of amino acid sequences.
countPatterns: Count patterns in sequences.
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.
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.
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.
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.
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