scPairs

0.1.8

Identifying Synergistic Gene Pairs in Single-Cell and Spatial Transcriptomics

0packages depend

2.3Kdownloads / year

40.8%test coverage

13/13checks pass

Overview

About

Maintained by Zhaoqing WangFirst published 2026-03-051 releasesCRAN page ↗GitHub ↗

Discovers synergistic gene pairs in single-cell RNA-seq and spatial transcriptomics data. Unlike conventional pairwise co-expression analyses that rely on a single correlation metric, scPairs integrates 14 complementary metrics across five orthogonal evidence layers to compute a composite synergy score with optional permutation-based significance testing. The five evidence layers span cell-level co-expression (Pearson, Spearman, biweight midcorrelation, mutual information, ratio consistency), neighbourhood-aware smoothing (KNN-smoothed correlation, neighbourhood co-expression, cluster pseudo-bulk, cross-cell-type, neighbourhood synergy), prior biological knowledge (GO/KEGG co-annotation Jaccard, pathway bridge score), trans-cellular interaction, and spatial co-variation (Lee's L, co-location quotient). This multi-scale design enables researchers to move beyond simple co-expression towards a comprehensive characterisation of cooperative gene regulation at transcriptomic and spatial resolution. For more information, see the package documentation at https://github.com/zhaoqing-wang/scPairs.

Install

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

install.packages("scPairs", 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("zhaoqing-wang/scPairs")

Development version from zhaoqing-wang/scPairs. 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-scpairs

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-scPairs

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-scPairs

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

Health

CRAN checks

13OK

Slowest check: 8.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.13

40.8%

Coverage · measured lines

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,111 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 98%
Return-value docs: 100%
References docs: 2%

Downloads

2.3K

CRAN downloads in the past year

Rank #8,008 · ~6/day · ~196/mo

Releases R versions

Daily download trend is not available in this view yet.

27830 days

1.3K90 days

2.3K1 year

Compare downloads with other packages →

Also on27 r2u15 autocran

Repository

GitHub ↗ zhaoqing-wang/scpairs

3Stars

0Forks

0Open issues

0Open PRs

5Releases

45Commits

1Contributors

45 commits · Last activity 2026-04-23

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/zhaoqing-wang/scpairs on 2026-07-26.

Reproducibility and dev environment (1)

data-raw/

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (13)

data.table ggplot2 ggraph ggrepel igraphmethodsMatrixpatchwork Seurat SeuratObjectstatstidygraph tidyr

LinkingTo (0)

none

Suggests (7)

AnnotationDbi org.Mm.eg.db org.Hs.eg.db crayon ggExtra RANN testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Zhaoqing Wang

Author, Maintainer

Authors (1)

Zhaoqing Wang

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.8Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-05
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 25 KB / 1 file
Download size: 136 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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