Package: alakazam
Type: Package
Version: 1.2.1
Date: 2022-09-19
Authors@R: c(person("Susanna", "Marquez", role=c("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("Jason", "Vander Heiden", role=c("cre", "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://bitbucket.org/kleinstein/alakazam/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
SystemRequirements: C++11
LinkingTo: Rcpp
biocViews: Software, AnnotationData
Depends: R (>= 4.0), ggplot2 (>= 3.3.4)
Imports: airr (>= 1.3), ape, dplyr (>= 1.0), graphics, grid, igraph (>=
        1.0), 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: 7.2.1
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'
NeedsCompilation: yes
Packaged: 2022-09-20 08:28:00 UTC; susanna
Author: Susanna Marquez [aut],
  Namita Gupta [aut],
  Nima Nouri [aut],
  Ruoyi Jiang [aut],
  Julian Zhou [aut],
  Kenneth Hoehn [aut],
  Daniel Gadala-Maria [ctb],
  Edel Aron [ctb],
  Jason Vander Heiden [cre, aut],
  Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-20 22:10:02 UTC
Built: R 4.1.3; x86_64-w64-mingw32; 2023-04-17 19:26:33 UTC; windows
Archs: i386, x64
