biocohort: Cohort Objects for Subjects and Samples in Omics Studies
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.
| Version: | 0.1.1 |
| 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 |
| Published: | 2026-09-18 |
| DOI: | 10.32614/CRAN.package.biocohort (may not be active yet) |
| Author: | Samuel Bharti 
[aut, cre, cph],
Barret Schloerke
[ths],
Carson Sievert
[ths],
Posit Software, PBC  [cph,
fnd] |
| Maintainer: | Samuel Bharti <samuelbharti.io at gmail.com> |
| BugReports: | https://github.com/samuelbharti/biocohort/issues |
| License: | MIT + file LICENSE |
| URL: | https://www.samuelbharti.com/biocohort/, https://github.com/samuelbharti/biocohort |
| NeedsCompilation: | no |
| SystemRequirements: | CrossMap (optional, for the CrossMap liftover backend) |
| Language: | en-US |
| Citation: | biocohort citation info |
| Materials: | README, NEWS |
| CRAN checks: | biocohort results |
Documentation:
| Reference manual: | biocohort.html , biocohort.pdf |
| Vignettes: |
Get started with biocohort (source, R code) Glossary (source, R code) Naming conventions (source, R code) |
Downloads:
| Package source: | biocohort_0.1.1.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): biocohort_0.1.1.tgz, r-release (x86_64): biocohort_0.1.1.tgz, r-oldrel (x86_64): biocohort_0.1.1.tgz |
Linking:
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