R Observatory: Metrics for pGRN version 0.3.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pGRN

0.3.5Package record

Single-Cell RNA Sequencing Pseudo-Time Based Gene Regulatory Network Inference

0packages depend

2.6Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Gangcai XieCRAN page ↗

Inference and visualize gene regulatory network based on single-cell RNA sequencing pseudo-time information.

Install

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

install.packages("pGRN", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-pgrn

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-pGRN

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-pGRN

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Gangcai Xie <gcxiester@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Gangcai",
                    family = "Xie",
                    role = c("aut", "cre"),
                    email = "gcxiester@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.5

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13
Examples that run: 100%12 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

pGRN HTML

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #18,849 · ~7/day · ~215/mo

Releases R versions

Daily download trend is not available in this view yet.

29630 days

69490 days

2.6K1 year

Compare downloads with other packages →

Also on64 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing pGRN adds 80 packages (45 with compiled code, 85 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 2.10

Imports (12)

bigmemory doParallel dtw foreach ggplot2 ggraph igraph lmtest proxy tidygraph visNetwork future

LinkingTo (0)

none

Suggests (3)

knitr webshot rmarkdown

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 (from the free-text Author field) (1)

Gangcai Xie

Maintainer since 0.3.5 (2023)

Releases (1)

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
R
R 4.3.0 released · 2023-04-21
0.3.5Latest
record
2023-01-17 · current release
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-17
Total releases: 1 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 9.0 KB / 1 file
Download size: 164 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pGRN")

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 pGRN version 0.3.5 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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