AnanseSeurat

1.2.0

Construct ANANSE GRN-Analysis Seurat

0packages depend

9Kdownloads / year

86.9%test coverage

13/13checks pass

Overview

About

Maintained by Jos SmitsFirst published 2023-01-252 releasesCRAN page ↗GitHub ↗

Enables gene regulatory network (GRN) analysis on single cell clusters, using the GRN analysis software 'ANANSE', Xu et al.(2021) doi:10.1093/nar/gkab598. Export data from 'Seurat' objects, for GRN analysis by 'ANANSE' implemented in 'snakemake'. Finally, incorporate results for visualization and interpretation.

Install

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

install.packages("AnanseSeurat", 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("JGASmits/AnanseSeurat")

Development version from JGASmits/AnanseSeurat. 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-ananseseurat

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

# 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-AnanseSeurat

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-AnanseSeurat

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.38

86.9%

Coverage · measured lines

91%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 259 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

CRAN downloads in the past year

Rank #4,571 · ~25/day · ~751/mo

Releases R versions

Daily download trend is not available in this view yet.

49530 days

2K90 days

9K1 year

Compare downloads with other packages →

Also on106 r2u34 autocran

Repository

GitHub ↗ jgasmits/ananseseurat

11Stars

3Forks

2Open issues

1Open PRs

4Releases

138Commits

4Contributors

single-cellsingle-cell-atac-seqsingle-cell-rna-seqgrn-analysisrseurat-objects

License Apache-2.0 · 138 commits · Last activity 2023-11-12 · 0% stars, 30d

Stars over time

2024-03-02 · 82026-07-07 · 11

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/jgasmits/ananseseurat on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.50

Imports (11)

dplyr ggplot2 ggpubr magrittr patchwork png purrr rlang Seurat stringrutils

LinkingTo (0)

none

Suggests (5)

covr knitr rmarkdown Signac testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,329 (65%)Rd 411 (20%)Vignettes 152 (7%)Other 121 (6%)YAML 20 (1%)

Code characteristics

Cyclomatic complexity: 6.0 median / 19 max
Test cases: 10 / 0.38 per code line

Test coverage

Line coverage

87%

Expression

88.7%

Tests / Examples

86.9% / 77% ex

Functions

10 10 exported

Complexity

6.7 avg / 19 max

Call network

10 nodes / 1 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

10 functions

Function	Cyclo	Coverage
per_cluster_df exp	4	64%
export_ATAC_maelstrom exp	6	72%
import_seurat_scANANSE exp	9	76%
import_seurat_maelstrom exp	6	80%
export_ATAC_scANANSE exp	4	82%
export_CPM_scANANSE exp	4	88%

People & History

People (2)

Maintainer (1)

Jos Smits

Author, Maintainer, Copyright holder

Authors (2)

Jos Smits

Author, Maintainer, Copyright holder

Huiqing Jo Zhou

Author, Funder, Copyright holder

Jos Smits

Author, Maintainer, Copyright holder

Huiqing Jo Zhou

Author, Funder, Copyright holder

Funders (1)

Huiqing Jo Zhou

Author, Funder, Copyright holder

Listed in earlier versions (1)

Zhou

no longer listed · 1.1.0 to 1.2.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.0Latest
2023-11-11 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.0
2023-01-25
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-25
Total releases: 2 / 3 yrs
License: Apache License (>= 2)
Minimum R: ≥ 3.50
Download size: 525 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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