Other packages > Find by keyword >

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]
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 10 May. 2025.
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
Downloads during the last 30 days
04/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/2004/2104/2204/2304/2404/2504/2604/2704/2804/2904/3005/0105/0205/0305/0405/0505/0605/0705/08Downloads for alakazam0100200300400500600700800900TrendBars

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
dataprep  
Efficient and Flexible Data Preprocessing Tools
Efficiently and flexibly preprocess data using a set of data filtering, deletion, and interpolation ...
Download / Learn more Package Citations See dependency  
distreg.vis  
Framework for the Visualization of Distributional Regression Models
Functions for visualizing distributional regression models fitted using the 'gamlss', 'bamlss' or 'b ...
Download / Learn more Package Citations See dependency  
hdpGLM  
Hierarchical Dirichlet Process Generalized Linear Models
Implementation of MCMC algorithms to estimate the Hierarchical Dirichlet Process Generalized Linear ...
Download / Learn more Package Citations See dependency  
specklestar  
Reduction of Speckle Data from BTA 6-m Telescope
A set of functions for obtaining positional parameters and magnitude difference between components o ...
Download / Learn more Package Citations See dependency  

24,205

R Packages

207,311

Dependencies

65,402

Author Associations

24,206

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA