Package: biocohort
Title: Cohort Objects for Subjects and Samples in Omics Studies
Version: 0.1.1
Authors@R: c(
    person("Samuel", "Bharti", , "samuelbharti.io@gmail.com",
           role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0003-4190-7058")),
    person("Barret", "Schloerke", , "barret@posit.co", role = "ths",
           comment = c(ORCID = "0000-0001-9986-114X")),
    person("Carson", "Sievert", , "carson@posit.co", role = "ths",
           comment = c(ORCID = "0000-0002-4958-2844")),
    person("Posit Software, PBC", role = c("cph", "fnd"),
           comment = c(ROR = "03wc8by49"))
  )
Description: Keeps the subjects, samples, and analysis outputs of a study in
    one validated object. It starts from a sample manifest with one row per
    sample, which is read, checked, and split into a subject table and a
    sample map. Species and assay are plain values in those tables rather
    than fixed types, so the same object serves any organism and any omics
    assay. From that object the package writes the sample sheet a pipeline
    expects, pairs tumor and normal samples on demand, and records where each
    analysis writes its output so the files can be loaded back in by subject
    or by pair. Manual corrections are kept in an audit trail. Results can
    also be translated across genome builds or species, with liftover for
    coordinates and ortholog mapping for genes.
License: MIT + file LICENSE
URL: https://www.samuelbharti.com/biocohort/,
        https://github.com/samuelbharti/biocohort
BugReports: https://github.com/samuelbharti/biocohort/issues
Encoding: UTF-8
Language: en-US
Depends: R (>= 4.1)
Imports: S7, cli, rlang, checkmate, fs, readr, dplyr (>= 1.1.0), tibble
Suggests: testthat (>= 3.0.0), pkgdown, knitr, rmarkdown, rtracklayer,
        GenomicRanges, IRanges, S4Vectors, babelgene, withr, readxl,
        writexl, arrow, SummarizedExperiment, SeuratObject, yaml
SystemRequirements: CrossMap (optional, for the CrossMap liftover
        backend)
VignetteBuilder: knitr
Config/testthat/edition: 3
LazyData: true
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-09-10 09:44:30 UTC; Samuel
Author: Samuel Bharti [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-4190-7058>),
  Barret Schloerke [ths] (ORCID: <https://orcid.org/0000-0001-9986-114X>),
  Carson Sievert [ths] (ORCID: <https://orcid.org/0000-0002-4958-2844>),
  Posit Software, PBC [cph, fnd] (ROR: <https://ror.org/03wc8by49>)
Maintainer: Samuel Bharti <samuelbharti.io@gmail.com>
Repository: CRAN
Date/Publication: 2026-09-18 11:20:14 UTC
