R Observatory: Metrics for biocohort version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biocohort

0.1.1Package record

Cohort Objects for Subjects and Samples in Omics Studies

0packages depend

496downloads / year

88.2%test coverage

13/13flavors OK

Overview

About

Maintained by Samuel BhartiCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Posit Software, PBC

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.

Changes in 0.1.1

Resubmission to CRAN. The package code is unchanged from 0.1.0; every change

is in the documentation and the repository.

?biocohort names the three articles as vignette() calls instead of linking to them by a relative path that only exists on the website, and the package README links to the contributing guide by its full URL. CRAN's pretest rejected 0.1.0 for both links.
The liftover_rtracklayer() example is wrapped in \donttest{}. Loading rtracklayer alone takes longer than the five seconds CRAN allows an example.
The Description field is rewritten in plainer sentences.
New examples for translate() on a cohort, translation_report(), load_analyses(), cohort_read(), register_liftover_backend(), register_ortholog_backend(), liftover_vcf(), and the Study, Subject, Cohort, AnalysisSpec, and TranslationResult constructors. The translation_report() example was a comment before, not code.

Show all changes in 0.1.1Hide the rest of the changes in 0.1.1

Help pages that still pointed to orthologize() now point to translate().
citation("biocohort") includes the Zenodo DOI.
README: install from r-universe as well as GitHub.
CI: a cran workflow runs the check the way CRAN's pretest does.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("biocohort", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("samuelbharti/biocohort")

Development version from samuelbharti/biocohort. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-biocohort

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-biocohort

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-biocohort

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK7 OK2026-09-19

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMEYes · 469 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.1.1Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 65includes a package overview page
Examples that run: 97%61 run in a plain check (1 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 98%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

496

CRAN downloads in the past year

Rank #24,079 · ~1/day · ~41/mo

Releases R versions

Daily download trend is not available in this view yet.

49630 days

49690 days

4961 year

Compare downloads with other packages →

Also on7 r2u29 autocran

How downloads are counted

Repository

samuelbharti/biocohort ↗Account: samuelbharti

3Stars

0Forks

11Open issues

1Open PRs

1Releases

215Commits

2Commit identities

License file reads as MIT · 215 commits · Last activity 2026-09-29

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 0

Issues over time

2026-09-19 · 02026-09-30 · 11

How these are measured

PracticesBeta

17 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/samuelbharti/biocohort on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (5)

Code of conductContributing guideIssue templatesPR templateSecurity policy

Docs source (2)

GitHub Pages site last deployed 2026-09-29 · The repository has a site deploy workflow

pkgdown site last built 2026-09-29

Coverage (1)

Coverage reporting

Show all practicesHide 4 practices

Research and citation (1)

CITATION.cff

Automation and maintenance (2)

Dependabotpre-commit

Lint, format, editor (3)

lintrLint workflowAir

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-02-05
Seen in the repository: .github/instructions
Pull request: opened by its own account
Commits: 8 by its own account
Claude Codefirst seen 2026-09-07
Named in .gitignore: .claude

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing biocohort adds 30 packages (18 with compiled code, 9.5 MB of source tarballs). Heaviest: fs 1.4 MB, vctrs 1.0 MB, dplyr 902 KB.

Depends (1)

R >= 4.1

Imports (8)

S7 cli rlang checkmate fs readr dplyr tibble

LinkingTo (0)

none

Suggests (16)

testthat pkgdown knitr rmarkdown rtracklayer GenomicRanges IRanges S4Vectors babelgene withr readxl writexl arrow SummarizedExperiment SeuratObject yaml

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Samuel Bharti

Posit Software, PBC

Copyright holder, Funder

Barret Schloerke

Thesis advisor

Carson Sievert

Thesis advisor

Releases (1)

0.1.1Latest
record
2026-09-18 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-09-18
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Bundled data: 20 KB / 1 file
Download size: 226 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("biocohort")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.5281/zenodo.22685057.

The repository also keeps a CITATION.cff.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for biocohort version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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