R Observatory: Metrics for Signac version 1.17.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Signac

1.17.1

Analysis of Single-Cell Chromatin Data

2packages depend

121.9Kdownloads / year

20.1%test coverage

13/13checks pass

Overview

About

Maintained by Tim StuartFirst published 2020-03-1323 releasesCRAN page ↗GitHub ↗

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) doi:10.1038/s41592-021-01282-5.

Install

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

install.packages("Signac", 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("stuart-lab/signac")

Development version from stuart-lab/signac. 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-signac

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: 10.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.05

20.1%

Coverage · measured lines

100%

Documentation · exports

31

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
OK2026-04-25
12 OK · 0 NOTE · 0 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

Show 3 earlier snapshots

NOTE2026-04-08
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-02
7 OK · 5 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
NOTE2026-03-10
8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 179 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 68%
Documented parameters: 100%
Return-value docs: 74%
References docs: 2%

Downloads

121.9K

CRAN downloads in the past year

Rank #1,327 · ~334/day · ~10.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

7.2K30 days

23.7K90 days

121.9K1 year

Compare downloads with other packages →

Also on877 r2u16K bioconda

Repository

GitHub ↗ stuart-lab/signac

424Stars

107Forks

1Open issues

0Open PRs

23Releases

2,225Commits

22Contributors

single-cellbioinformaticsatac

2,225 commits · Last activity 2026-08-05 · +0.5% stars, 30d

Stars over time

2026-07-11 · 4212026-07-22 · 424

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/stuart-lab/signac on 2026-08-09.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Dockerfile

Governance and community (1)

Issue templates

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

44 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1.0methods

LinkingTo (1)

Rcpp

Suggests (18)

Seurat ggforce ggrepel ggseqlogo testthat (>= 2.1.0)SummarizedExperiment TFBSTools motifmatchr BSgenome shiny miniUI rtracklayer biovizBase Biostrings lsaMASSwrswoR fgsea

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

AnanseSeurat SeuratExplorer

Code & Tests

People & History

People (4)

Maintainer (1)

Tim Stuart

Author, Maintainer

Authors (2)

Tim Stuart

Author, Maintainer

Avi Srivastava

Author · added in 1.0.0

Contributors (2)

Paul Hoffman

Contributor

Rahul Satija

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.17.1Latest
2026-04-07 · current release · diff ↗
1.17.0
2026-04-01 · diff ↗
1.16.0
2025-10-10 · diff ↗
1.15.0
2025-08-18 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.14.0
2024-08-21 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.13.0
2024-04-04 · diff ↗
1.12.0
2023-11-08 · diff ↗
1.11.0
2023-10-13 · diff ↗
1.10.0
2023-05-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.9.0
2022-12-08 · diff ↗
1.8.0
2022-09-21 · diff ↗
1.7.0
2022-06-01 · diff ↗

Show 15 earlier events

R
R 4.2.0 released · 2022-04-22
1.6.0
2022-03-05 · diff ↗
1.5.0
2021-12-08 · diff ↗
1.4.0
2021-09-22 · diff ↗
1.3.0
2021-07-12 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.1
2021-05-11 · diff ↗
1.2.0
2021-04-28 · diff ↗
1.1.1
2021-02-04 · diff ↗
1.1.0
2020-11-07 · diff ↗
1.0.0
2020-08-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.5
2020-04-16 · diff ↗
0.2.4
2020-03-13
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-13
Total releases: 23 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 473 KB / 9 files
Download size: 3.8 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("Signac")

Format

Stuart, T., Hoffman, P., Satija, R., & Srivastava, A. (2026). Signac: Analysis of Single-Cell Chromatin Data (Version 1.17.1) [Computer software]. https://doi.org/10.32614/CRAN.package.Signac

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 Signac version 1.17.1 [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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