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alakazam  

Immunoglobulin Clonal Lineage and Diversity Analysis
View on CRAN: Click here


Download and install alakazam package within the R console
Install from CRAN:
install.packages("alakazam")

Install from Github:
library("remotes")
install_github("cran/alakazam")

Install by package version:
library("remotes")
install_version("alakazam", "1.3.0")



Attach the package and use:
library("alakazam")
Maintained by
Susanna Marquez
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-01-29
Latest Update: 2023-09-30
Description:
Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) , Stern, Yaari and Vander Heiden, et al (2014) .
How to cite:
Susanna Marquez (2016). alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis. R package version 1.3.0, https://cran.r-project.org/web/packages/alakazam. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.2.2 (2016-01-29 22:26), 0.2.3 (2016-02-22 22:49), 0.2.4 (2016-07-29 00:32), 0.2.5 (2016-08-06 00:19), 0.2.6 (2017-03-23 07:17), 0.2.7 (2017-06-15 17:47), 0.2.8 (2017-09-21 21:29), 0.2.9 (2018-03-22 21:16), 0.2.10 (2018-03-30 19:29), 0.2.11 (2018-09-14 18:10), 0.3.0 (2019-07-18 13:20), 1.0.0 (2020-05-08 19:30), 1.0.1 (2020-05-11 20:10), 1.0.2 (2020-07-19 02:30), 1.1.0 (2021-02-07 07:00), 1.2.0 (2021-11-01 17:10), 1.2.1 (2022-09-21 00:10)
Other packages that cited alakazam R package
View alakazam citation profile
Other R packages that alakazam depends, imports, suggests or enhances
Complete documentation for alakazam
Functions, R codes and Examples using the alakazam R package
Some associated functions: ABBREV_AA . AbundanceCurve-class . ChangeoClone-class . DEFAULT_COLORS . DiversityCurve-class . EdgeTest-class . Example10x . ExampleDb . ExampleDbChangeo . ExampleTrees . IMGT_REGIONS . IUPAC_CODES . MRCATest-class . SingleDb . alakazam-package . alakazam . aliphatic . alphaDiversity . aminoAcidProperties . baseTheme . buildPhylipLineage . bulk . calcCoverage . calcDiversity . charge . checkColumns . collapseDuplicates . combineIgphyml . countClones . countGenes . countPatterns . cpuCount . estimateAbundance . extractVRegion . getAAMatrix . getDNAMatrix . getMRCA . getPathLengths . getPositionQuality . getSegment . graphToPhylo . gravy . gridPlot . groupGenes . isValidAASeq . junctionAlignment . makeChangeoClone . makeTempDir . maskPositionsByQuality . maskSeqEnds . maskSeqGaps . nonsquareDist . padSeqEnds . pairwiseDist . pairwiseEqual . permuteLabels . phyloToGraph . plotAbundanceCurve . plotDiversityCurve . plotDiversityTest . plotEdgeTest . plotMRCATest . plotSubtrees . polar . progressBar . rarefyDiversity . readChangeoDb . readFastqDb . readIgphyml . seqDist . seqEqual . sortGenes . stoufferMeta . summarizeSubtrees . tableEdges . testDiversity . testEdges . testMRCA . translateDNA . translateStrings . writeChangeoDb . 
Some associated R codes: Alakazam.R . AminoAcids.R . Classes.R . Core.R . Data.R . Deprecated.R . Diversity.R . Fastq.R . Gene.R . Lineage.R . RcppExports.R . Sequence.R . Topology.R .  Full alakazam package functions and examples
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