Package: biocohort
Title: Cohort Objects for Subjects and Samples in Omics Studies
Version: 0.1.1.9000
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
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.1)
Imports: S7, cli (>= 3.2.0), 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: 8.1.0
Config/pak/sysreqs: cmake make libuv1-dev libx11-dev
Repository: https://samuelbharti.r-universe.dev
Date/Publication: 2026-09-29 22:52:20 UTC
RemoteUrl: https://github.com/samuelbharti/biocohort
RemoteRef: HEAD
RemoteSha: a7c03ed100fb348800e08038c6eaf52e89ba8cc9
RemoteSubdir: pkg-r
NeedsCompilation: no
Packaged: 2026-10-30 07:37:27 UTC; root
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>