R Observatory: Metrics for SignacX version 2.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SignacX

2.2.5Package record

Cell Type Identification and Discovery from Single Cell Gene Expression Data

0packages depend

3.4Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Mathew ChamberlainCRAN page ↗GitHub ↗Issues ↗Declared funder: Sanofi US

An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) doi:10.1101/2021.02.01.429207 for more details.

Changes in 2.2.5

Fixed issues with rhdf5 library that caused problems hosting SignacX on CRAN. Previously, SignacX looked to import an s3 method from rhdf5, which was changed to an importable method for saving hdf5 files.

From NEWS.md in the release

Install

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

install.packages("SignacX", 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("mathewchamberlain/SignacX")

Development version from mathewchamberlain/SignacX. 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-signacx

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-SignacX

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-SignacX

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: ‘Mathew Chamberlain <chamberlainphd@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 2.2 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 NOTE2026-04-10
ERROR12 OK, 1 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.5

READMEYes · 1,895 wordsVignettesYes · 7 · dynamicNEWSYes · 67% structured · mentions 2.2.5Citation fileYes · cites a publication

Help pages: 21 (1 internal)
Examples that run: 6%1 run in a plain check · 17 never run
Exported functions with examples: 95%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

Vignettes (7)

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #12,103 · ~9/day · ~281/mo

Releases R versions

Daily download trend is not available in this view yet.

33330 days

90490 days

3.4K1 year

Compare downloads with other packages →

Also on102 r2u3 autocran47 c2d4u

How downloads are counted

Repository

mathewchamberlain/signacx ↗Account: mathewchamberlain

28Stars

6Forks

10Open issues

0Open PRs

15Releases

147Commits

1Commit identities

seuratcellular-phenotypessingle-cell-rna-seq

License file reads as GPL-3.0 · 147 commits · Last activity 2023-02-28 · 0% stars, 30d · The default branch showed an older version (2.2.0) than CRAN on 2026-10-18 · Discussions: 3 posts

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 474

Stars over time

2026-07-11 · 272026-07-28 · 28

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/mathewchamberlain/signacx on 2026-10-18.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2023-02-28

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing SignacX adds 145 packages (88 with compiled code, 136 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.5.0

Imports (11)

neuralnet lme4methodsMatrixpbmcapply Seurat RJSONIO igraph jsonlite RColorBrewer (>= 1.1.2)stats

LinkingTo (0)

none

Suggests (5)

hdf5r rhdf5 knitr rmarkdown formatR

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 (6)

Mathew Chamberlain

Author, Maintainer since 2.2.0 (2021)

Author

Author

Author

Author

Funder

Releases (6)

Pick two releases to compare their code metrics.

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
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-11-18
2.2.5Latest
record
2021-11-18 · current release · diff ↗
archivedRemoved from CRAN
2021-11-17
check problems were not corrected in time
2.2.4
record
2021-07-22 · diff ↗
2.2.3
record
2021-07-16 · diff ↗
2.2.2
record
2021-06-24 · diff ↗
2.2.1
record
2021-06-17 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.2.0
record
2021-03-01
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-03-01
Total releases: 6 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 13 KB / 1 file
Download size: 2.3 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("SignacX")

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

It points to 10.1101/2021.02.01.429207.

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 SignacX version 2.2.5 [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.

Report a problem with this page →