cinaR

0.2.6

A Computational Pipeline for Bulk 'ATAC-Seq' Profiles

0packages depend

2.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Onur KarakaslarFirst published 2020-11-145 releasesCRAN page ↗GitHub ↗

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.

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.

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

Health

CRAN checks

13OK

Slowest check: 3.7 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 262 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 36%
Documented parameters: 100%
Return-value docs: 94%
References docs: 9%

Downloads

2.9K

CRAN downloads in the past year

Rank #12,530 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

28630 days

85390 days

2.9K1 year

Compare downloads with other packages →

Also on227 r2u

Repository

GitHub ↗ eonurk/cinar

16Stars

4Forks

1Open issues

0Open PRs

0Releases

168Commits

6Contributors

atac-seqdifferential-analysisenrichment-analysisgene-sets

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

Stars over time

2024-12-31 · 132026-07-07 · 16

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/eonurk/cinar on 2026-07-19.

Continuous integration (2)

GitHub ActionsTravis CI

Docs source (1)

README.Rmd

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 1,950 (62%)Rd 828 (26%)Vignettes 368 (12%)

Code characteristics

Cyclomatic complexity: 4.0 median / 34 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

22 15 exported

Complexity

7.7 avg / 34 max

Call network

22 nodes / 17 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 4

Name	Class	Rows × Cols	Also ships in
bed	data.frame	1,000 × 25	–
grch37	tbl_df/tbl/data.frame	66,978 × 3	–
grch38	tbl_df/tbl/data.frame	67,495 × 3	in 2 packages
grcm38	data.frame	25,350 × 4	–

People & History

People (2)

Maintainer (1)

Onur Karakaslar

Author, Maintainer

Authors (2)

Onur Karakaslar

Author, Maintainer

Duygu Ucar

Author

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.2.6Latest
2026-02-04 · current release · diff ↗
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
0.2.3
2022-05-18 · diff ↗
unarchivedReturned to CRAN
2022-05-18
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
0.2.1
2021-04-02 · diff ↗
unarchivedReturned to CRAN
2021-04-02
archivedRemoved from CRAN
2021-03-30
check problems were not corrected in time
0.2.0
2021-01-05 · diff ↗
0.1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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