R Observatory: Metrics for SignacX version 2.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SignacX

2.2.5

Cell Type Identification and Discovery from Single Cell Gene Expression Data

0packages depend

3.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Mathew ChamberlainFirst published 2021-03-016 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

11

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,895 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 6%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

3.3K

CRAN downloads in the past year

Rank #12,559 · ~9/day · ~277/mo

Releases R versions

Daily download trend is not available in this view yet.

21530 days

79590 days

3.3K1 year

Compare downloads with other packages →

Also on126 r2u26 c2d4u

Repository

GitHub ↗ mathewchamberlain/signacx

28Stars

6Forks

10Open issues

0Open PRs

15Releases

147Commits

1Contributors

seuratcellular-phenotypessingle-cell-rna-seq

License GPL-3.0 · 147 commits · Last activity 2023-03-06 · +3.7% stars, 30d

Stars over time

2026-07-11 · 272026-07-28 · 28

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/mathewchamberlain/signacx on 2026-08-16.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Mathew Chamberlain

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Funders (1)

Sanofi US

Funder

Package Timeline

6 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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.2.5Latest
2021-11-18 · current release · diff ↗
unarchivedReturned to CRAN
2021-11-18
archivedRemoved from CRAN
2021-11-17
check problems were not corrected in time
2.2.4
2021-07-22 · diff ↗
2.2.3
2021-07-16 · diff ↗
2.2.2
2021-06-24 · diff ↗
2.2.1
2021-06-17 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.2.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SignacX")

Format

Chamberlain, M., Sanofi US, Hanamsagar, R., Nestle, F., Savova, V., & de Rinaldis, E. (2021). SignacX: Cell Type Identification and Discovery from Single Cell Gene Expression Data (Version 2.2.5) [Computer software]. https://doi.org/10.32614/CRAN.package.SignacX

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, 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 →