R Observatory: Metrics for inferCSN version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

inferCSN

1.2.0Package record

Inferring Cell-Specific Gene Regulatory Network

0packages depend

3.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Meng XuCRAN page ↗GitHub ↗Website ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-22

Show 3 earlier changesHide 3 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-30
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.0

READMEYes · 79 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 37 (1 internal)includes a package overview page
Examples that run: 97%30 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 94%
Help pages citing references: 5%

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #10,725 · ~9/day · ~267/mo

Releases R versions

Daily download trend is not available in this view yet.

41430 days

96590 days

3.2K1 year

Compare downloads with other packages →

Also on609 r2u5 autocran

How downloads are counted

Repository

mengxu98/infercsn ↗Account: mengxu98

7Stars

0Forks

0Open issues

0Open PRs

0Releases

845Commits

1Commit identities

845 commits · Last activity 2026-10-14 · 0% stars, 30d · Default branch at 1.2.5, ahead of CRAN 1.2.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 73
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-15 · 42026-07-07 · 7

How these are measured

PracticesBeta

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

Checks run against github.com/mengxu98/infercsn on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-14 · The repository has a site deploy workflow

pkgdown site last built 2026-10-14

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

renv

Show all practicesHide 1 practice

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

32 external dependencies (excludes base and recommended)

Installing inferCSN adds 61 packages (40 with compiled code, 57 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Meng Xu

Author, Maintainer since 0.99.0 (2023)

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.0Latest
record
2025-10-16 · current release · diff ↗ ·
removed 12 exports
%ss%, as_matrix, check_sparsity, log_message, matrix_to_table, normalization, parallelize_fun, simulate_sparse_matrix, sparse_cor, sparse_regression, split_indices, table_to_matrix

added 1 export
infercsn_logo
R
R 4.5.0 released · 2025-04-11
1.1.7
record
2025-03-30 · diff ↗
1.1.6
record
2025-03-27 · diff ↗ ·
removed 3 exports
calculate_acc, fit_sparse_regression, plot_weight_distribution

added 22 exports
%ss%, calculate_accuracy, calculate_auprc, calculate_auroc, calculate_f1, calculate_ji, calculate_metrics, calculate_precision, calculate_recall, calculate_si, fit_srm, matrix_to_table, meta_cells, plot_coefficient, plot_coefficients, plot_edges_comparison, plot_histogram, simulate_sparse_matrix, sparse_cor, split_indices, subsampling, weight_sift
1.0.8
record
2024-08-24 · diff ↗ ·
removed 10 exports
acc.calculate, auc.calculate, calculate.gene.rank, check.parameters, model.fit, network.heatmap, prepare.performance.data, single.network, sparse.regression, table.to.matrix

added 12 exports
calculate_acc, calculate_auc, calculate_gene_rank, check_sparsity, fit_sparse_regression, log_message, plot_embedding, plot_network_heatmap, plot_weight_distribution, single_network, sparse_regression, table_to_matrix
1.0.5
record
2024-06-26 · diff ↗ ·
removed 6 exports
contrast.networks, crossweight, crossweight_params, dynamic.networks, net.format, weight_filter

added 8 exports
as_matrix, network_format, network_sift, parallelize_fun, plot_contrast_networks, plot_dynamic_networks, plot_scatter, plot_static_networks
R
R 4.4.0 released · 2024-04-24
1.0.3
record
2024-04-17 · diff ↗ ·
removed 1 export
filter.sort.matrix

added 5 exports
crossweight, crossweight_params, filter_sort_matrix, normalization, weight_filter
1.0.1
record
2024-03-15 · diff ↗ ·
removed 3 exports
compute.gene.rank, inferCSN.fit, sub.inferCSN

added 4 exports
calculate.gene.rank, filter.sort.matrix, model.fit, single.network
1.0.0
record
2024-02-09 · diff ↗ ·
removed 1 export
is.scalar
0.99.9
record
2024-01-10 · diff ↗ ·
added 2 exports
prepare.performance.data, table.to.matrix
0.99.8
record
2023-12-04 · diff ↗
0.99.7
record
2023-10-30 · diff ↗
0.99.6
record
2023-10-27 · diff ↗
0.99.0
record
2023-10-11

Show 1 earlier eventHide 1 earlier event

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

Cite

Cite this package

Run in R for the authors' entry:

citation("inferCSN")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1038/s41540-023-00267-8, 10.1287/opre.2019.1919.

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 inferCSN version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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