Package: VDJdive
Title: Analysis Tools for 10X V(D)J Data
Version: 1.10.0
Authors@R: c(
    person("Kelly", "Street", role = c("aut", "cre"), email = "street.kelly@gmail.com", comment = c(ORCID = "0000-0001-6379-5013")),
    person("Mercedeh", "Movassagh", role = "aut", email = "mercedeh@ds.dfci.harvard.edu", comment = c(ORCID = "0000-0001-7690-0230")),
    person("Jill", "Lundell", role = "aut", email = "jflundell@gmail.com", comment = c(ORCID = "0000-0002-6048-4700")),
    person("Jared", "Brown", role = "ctb"),
    person("Linglin", "Huang", role = "ctb"),
    person("Mingzhi", "Ye", role = "ctb"))
Description: This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.
Depends: R (>= 4.2)
Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix,
        methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
        stats, SummarizedExperiment, utils
Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
LinkingTo: Rcpp
License: Artistic-2.0
URL: https://github.com/kstreet13/VDJdive
BugReports: https://github.com/kstreet13/VDJdive/issues
biocViews: Software, ImmunoOncology, SingleCell, Annotation, RNASeq,
        TargetedResequencing
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
StagedInstall: no
VignetteBuilder: knitr
Collate: 'RcppExports.R' 'clonoStats_class.R' 'abundanceVDJ.R'
        'barVDJ.R' 'boxVDJ.R' 'calculateDiversity.R'
        'clonoStats_helpers.R' 'clonoStats.R' 'contigs.R' 'pieVDJ.R'
        'runBreakaway.R' 'runVDJPCA.R' 'scatterVDJ.R' 'setup.R'
        'utils.R'
git_url: https://git.bioconductor.org/packages/VDJdive
git_branch: RELEASE_3_21
git_last_commit: 525da39
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-16 04:21:34 UTC; biocbuild
Author: Kelly Street [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-6379-5013>),
  Mercedeh Movassagh [aut] (ORCID:
    <https://orcid.org/0000-0001-7690-0230>),
  Jill Lundell [aut] (ORCID: <https://orcid.org/0000-0002-6048-4700>),
  Jared Brown [ctb],
  Linglin Huang [ctb],
  Mingzhi Ye [ctb]
Maintainer: Kelly Street <street.kelly@gmail.com>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 15:47:17 UTC; windows
Archs: x64
