inferCSN

1.2.0

Inferring Cell-Specific Gene Regulatory Network

0packages depend

3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Meng XuFirst published 2023-10-1113 releasesCRAN page ↗GitHub ↗

An R package for inferring cell-type specific gene regulatory network from single-cell RNA-seq data.

Install

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

install.packages("inferCSN", 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("mengxu98/inferCSN")

Development version from mengxu98/inferCSN. 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-infercsn

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-inferCSN

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-inferCSN

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

Health

CRAN checks

13OK

Slowest check: 5.9 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

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-30
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 79 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 96%
Return-value docs: 94%
References docs: 5%

Downloads

CRAN downloads in the past year

Rank #14,225 · ~8/day · ~252/mo

Releases R versions

Daily download trend is not available in this view yet.

21730 days

77490 days

3K1 year

Compare downloads with other packages →

Also on656 r2u32 autocran

Repository

GitHub ↗ mengxu98/infercsn

7Stars

0Forks

0Open issues

0Open PRs

0Releases

810Commits

1Contributors

810 commits · Last activity 2026-01-23 · 0% stars, 30d

Stars over time

2023-11-20 · 32026-07-07 · 7

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mengxu98/infercsn on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

renv

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (12)

cli dplyr ggnetwork ggplot2 ggraph L0LearnMatrixmethodspurrr Rcppstatsthisutils

LinkingTo (1)

Rcpp

Suggests (22)

ComplexHeatmap circlize gtools gganimate ggExtra ggpointdensity ggpubr igraph irlba network patchwork plotly precrec pROC proxy tidygraph RANN RColorBrewer Rtsne RTransferEntropy uwot viridis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 4,267 (61%)Rd 1,942 (28%)C++ 716 (10%)C 21 (0%)

Code characteristics

Object systems

S31S4 generic1S4 method3

Cyclomatic complexity: 2.0 median / 29 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

55 30 exported

Complexity

4.2 avg / 29 max

Call network

55 nodes / 42 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
example_ground_truth	data.frame	19 × 4	–
example_meta_data	data.frame	5,000 × 2	–

People & History

People (1)

Maintainer (1)

Meng Xu

Author, Maintainer

Authors (1)

Meng Xu

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.0Latest
2025-10-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.7
2025-03-30 · diff ↗
1.1.6
2025-03-27 · diff ↗
1.0.8
2024-08-24 · diff ↗
1.0.5
2024-06-26 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.3
2024-04-17 · diff ↗
1.0.1
2024-03-15 · diff ↗
1.0.0
2024-02-09 · diff ↗
0.99.9
2024-01-10 · diff ↗
0.99.8
2023-12-04 · diff ↗
0.99.7
2023-10-30 · diff ↗
0.99.6
2023-10-27 · diff ↗
0.99.0
2023-10-11

Show 1 earlier events

R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-11
Total releases: 13 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 733 KB / 3 files
Download size: 820 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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