DESCRIPTION

Package: alakazam
Type: Package
Version: 1.3.1.999
Date: 2024-08-01
Authors@R: c(person("Susanna", "Marquez", role=c("cre", "aut"), 
                    email="susanna.marquez@yale.edu"),
             person("Namita", "Gupta", role=c("aut"), 
                    email="namita.gupta@yale.edu"),
             person("Nima", "Nouri", role=c("aut"), 
                    email="nima.nouri@yale.edu"),
             person("Ruoyi", "Jiang", role=c("aut"), 
                    email="ruoyi.jiang@yale.edu"),
             person("Julian", "Zhou", role=c("aut"), 
                    email="julian.zhou@bulldogs.yale.edu"),
             person("Kenneth", "Hoehn", role=c("aut"), 
                    email="kenneth.hoehn@yale.edu"),
             person("Daniel", "Gadala-Maria", role=c("ctb"), 
                    email="daniel.gadala-maria@yale.edu"),
             person("Edel", "Aron", role=c("ctb"), 
                    email="edel.aron@yale.edu"),
             person("Cole", "Jensen", role=c("ctb"),
                    email="cole.jensen@yale.edu"),
             person("Gisela", "Gabernet", role=c("ctb"),
                    email="gisela.gabernet@yale.edu"),
             person("Jason", "Vander Heiden", role=c("aut"), 
                    email="jason.vanderheiden@gmail.com"), 
             person("Steven", "Kleinstein", role=c("aut", "cph"), 
                    email="steven.kleinstein@yale.edu"))
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
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) <doi:10.1093/bioinformatics/btv359>,
    Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
License: AGPL-3
URL: https://alakazam.readthedocs.io/
BugReports: https://github.com/immcantation/alakazam/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
LinkingTo: Rcpp
biocViews:
    Software,
    AnnotationData
Depends:
    R (>= 4.0),
    ggplot2 (>= 3.4.0)
Imports:
    airr (>= 1.4.1),
    ape,
    dplyr (>= 1.0),
    graphics,
    grid,
    igraph (>= 1.5.0),
    Matrix (>= 1.3-0),
    methods,
    progress,
    Rcpp (>= 0.12.12),
    readr,
    rlang,
    scales,
    seqinr,
    stats,
    stringi,
    tibble,
    tidyr (>= 1.0),
    utils,
    Biostrings (>= 2.56.0),
    GenomicAlignments (>= 1.24.0),
    IRanges (>= 2.22.2)
Suggests:
    knitr,
    rmarkdown,
    testthat
RoxygenNote: 7.3.2
Collate: 
    'Alakazam.R'
    'AminoAcids.R'
    'Classes.R'
    'Core.R'
    'Data.R'
    'Diversity.R'
    'Deprecated.R'
    'Fastq.R'
    'Gene.R'
    'Lineage.R'
    'RcppExports.R'
    'Sequence.R'
    'Topology.R'