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biocohort  

Cohort Objects for Subjects and Samples in Omics Studies
View on CRAN: Click here


Download and install biocohort package within the R console
Install from CRAN:
install.packages("biocohort")

Install from Github:
library("remotes")
install_github("cran/biocohort")

Install by package version:
library("remotes")
install_version("biocohort", "0.1.1")



Attach the package and use:
library("biocohort")
Maintained by
Samuel Bharti
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-09-18
Latest Update: 2026-09-18
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.
How to cite:
Samuel Bharti (2026). biocohort: Cohort Objects for Subjects and Samples in Omics Studies. R package version 0.1.1, https://cran.r-project.org/web/packages/biocohort. Accessed 02 Nov. 2026.
Previous versions and publish date:
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Complete documentation for biocohort
Functions, R codes and Examples using the biocohort R package
Full biocohort package functions and examples
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