R Observatory: Metrics for conos version 1.5.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

conos

1.5.4

Clustering on Network of Samples

3packages depend

8.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Evan BiederstedtFirst published 2021-02-2315 releasesCRAN page ↗GitHub ↗

Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at https://github.com/kharchenkolab/conos. The size of the 'conosPanel' package is approximately 12 MB.

Install

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

install.packages("conos", 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("kharchenkolab/conos")

Development version from kharchenkolab/conos. 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-conos

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: 9.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

100%

Documentation · exports

25

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 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
OK2026-04-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

WARNING2026-04-23
8 OK · 3 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
10 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
9 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,176 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 66%
References docs: 0%

Downloads

8.9K

CRAN downloads in the past year

Rank #4,106 · ~24/day · ~740/mo

Releases R versions

Daily download trend is not available in this view yet.

49430 days

2.1K90 days

8.9K1 year

Compare downloads with other packages →

Also on440 r2u2.5K bioconda28 c2d4u

Repository

GitHub ↗ kharchenkolab/conos

230Stars

40Forks

8Open issues

2Open PRs

20Releases

1,115Commits

13Contributors

scrna-seqsingle-cell-rna-seqbatch-correction

License GPL-3.0 · 1,115 commits · Last activity 2026-07-02 · +0.4% stars, 30d

Stars over time

2025-06-28 · 2122026-08-04 · 230

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/kharchenkolab/conos on 2026-08-09.

Continuous integration (1)

CircleCI

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

48 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.5.0Matrixigraph

Imports (23)

abind cowplot ComplexHeatmap dendextend dplyr ggplot2 ggrepel gridExtra irlba leidenAlg magrittrmethodsN2R pagoda2parallelR6 reshape2 rlang Rtsne sccore (>= 1.0.0)statstoolsutils

LinkingTo (4)

Rcpp RcppArmadillo RcppEigen RcppProgress

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

CRMetrics lstar scITD

Code & Tests

People & History

People (5)

Maintainer (1)

Evan Biederstedt

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Contributors (1)

Weiliang Qiu

Contributor

Package Timeline

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

1.5.4Latest
2026-04-25 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.5.3
2026-04-02 · diff ↗
unarchivedReturned to CRAN
2026-04-01
archivedRemoved from CRAN
2026-03-13
requires archived package 'N2R'
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.5.2
2024-02-26 · diff ↗
1.5.1
2024-01-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.5.0
2022-10-17 · diff ↗
1.4.9
2022-09-30 · diff ↗
1.4.8
2022-09-26 · diff ↗
1.4.7
2022-09-04 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.4.6
2022-04-12 · diff ↗

Show 8 earlier events

1.4.5
2022-01-21 · diff ↗
1.4.4
2021-11-08 · diff ↗
1.4.3
2021-08-08 · diff ↗
1.4.2
2021-06-29 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.4.1
2021-05-15 · diff ↗
1.4.0
2021-02-23
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-02-23
Total releases: 15 / 5 yrs
License: GPL-3 OSI
Additional repositories: kharchenkolab.github.io
Minimum R: ≥ 3.5.0
Bundled data: 500 KB / 1 file
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("conos")

Format

Biederstedt, E., Barkas, N., Kharchenko, P., Petukhov, V., & Qiu, W. (2026). conos: Clustering on Network of Samples (Version 1.5.4) [Computer software]. https://doi.org/10.32614/CRAN.package.conos

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 conos version 1.5.4 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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