R Observatory: Metrics for cinaR version 0.2.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cinaR

0.2.6Package record

A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

0packages depend

3.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Onur KarakaslarCRAN page ↗GitHub ↗Website ↗Issues ↗

Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) doi:10.1101/2021.03.05.434143.

Changes in 0.2.6

Fixed plotting helpers (pheatmap ..., dot-plot scale, PCA palette)
Wired norm.method/filter.method into the pipeline
Made run_enrichment() more robust to input shape and empty contrasts
Added prep_scATAC_seurat() helper for Seurat/Signac objects

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("cinaR", 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("eonurk/cinaR")

Development version from eonurk/cinaR. 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-cinar

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 5 earlier changesHide 5 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.6

READMEYes · 262 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.6Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 23
Examples that run: 36%5 run in a plain check · 8 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 81%
Documented parameters: 100%
Return-value docs: 94%
Help pages citing references: 9%

Vignettes (1)

cinaR

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #10,231 · ~9/day · ~275/mo

Releases R versions

Daily download trend is not available in this view yet.

37530 days

99790 days

3.3K1 year

Compare downloads with other packages →

Also on200 r2u

How downloads are counted

Repository

eonurk/cinar ↗Account: eonurk

16Stars

4Forks

1Open issues

0Open PRs

0Releases

168Commits

6Commit identities

atac-seqdifferential-analysisenrichment-analysisgene-sets

168 commits · Last activity 2026-02-09 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 534

Stars over time

2025-08-20 · 142026-07-07 · 16

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/eonurk/cinar on 2026-10-22.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on macOS

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-09 · The repository has a site deploy workflow

pkgdown site last built 2026-02-09

For agents and models (1)

llms.txt

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing cinaR adds 30 packages (15 with compiled code, 19 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB. 7 more not on CRAN are not measured.

Depends (1)

R >= 4.0.0

Imports (17)

BiocManager DESeq2 dplyr edgeR fgsea GenomicRanges ggplot2 ggrepelgrDeviceslimmamethodsutilspheatmap preprocessCore RColorBrewer sva writexl

LinkingTo (0)

none

Suggests (9)

ChIPseeker knitrMatrixSeurat rmarkdown markdown TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene

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 (2)

Onur Karakaslar

Author, Maintainer since 0.1.0 (2020)

Duygu Ucar

Author

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.2.6Latest
record
2026-02-04 · current release · diff ↗ ·
added 2 exports
prep_scATAC_cinaR, prep_scATAC_seurat
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-05-18
0.2.3
record
2022-05-18 · diff ↗ ·
removed 1 export
mouse2human
archivedRemoved from CRAN
2022-04-26
repeated policy violations On Internet access, warned in 2022-02
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2021-04-02
0.2.1
record
2021-04-02 · diff ↗ ·
added 1 export
verboseFn
archivedRemoved from CRAN
2021-03-30
check problems were not corrected in time
0.2.0
record
2021-01-05 · diff ↗ ·
removed 1 export
heatmap_plot

added 4 exports
heatmap_differential, heatmap_var_peaks, scale_rows, show_comparisons
0.1.0
record
2020-11-14
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-14
Total releases: 5 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 1.2 MB / 5 files
Download size: 2.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("cinaR")

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

It points to 10.1101/2021.03.05.434143.

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 cinaR version 0.2.6 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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