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stance

Cell type-specific SVG detection

https://github.com/cui-stt-lab/stance

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Cell type-specific SVG detection

Basic Info
  • Host: GitHub
  • Owner: Cui-STT-Lab
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 15.5 MB
Statistics
  • Stars: 6
  • Watchers: 4
  • Forks: 2
  • Open Issues: 2
  • Releases: 1
Created almost 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

STANCE: Spatial Transcriptomics ANalysis of genes with Cell-type-specific Expression

STANCE flowchart

STANCE is a unified statistical model to detect cell type-specific spatially variable genes (ctSVGs) in spatial transcriptomics. By integrating gene expression, spatial location, and cell type composition through a linear mixed-effect model, STANCE enables the identification of both SVGs and ctSVGs in an initial stage, followed by a second stage test dedicated to ctSVG detection. Its design ensures robustness in complex scenarios and the results are spatial rotation invariant.

Reference: Su, H., Wu, Y., Chen, B. and Cui, Y. STANCE: a unified statistical model to detect cell-type-specific spatially variable genes in spatial transcriptomics. Nat Commun 16, 1793 (2025). https://doi.org/10.1038/s41467-025-57117-w

Installation

Please run the following codes in R to install STANCE package from GitHub. if (!require("devtools", quietly = TRUE)){ install.packages("devtools") } devtools::install_github("Cui-STT-Lab/STANCE")

STANCE relies on several packages, including gaston, KRLS, SPARK, among others, most of which are installed automatically. If automatic installation fails, you can manually install them in R by running the following codes: install.packages("gaston") install.packages("KRLS") if (!require("devtools", quietly = TRUE)){ install.packages("devtools") } devtools::install_github("xzhoulab/SPARK") library(SPARK)

Detect cell type-specific spatially variable genes (ctSVGs) with STANCE

The best vignette for getting started with STANCE is Tutorial.

Owner

  • Login: Cui-STT-Lab
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Su
    given-names: Haohao
    orcid: https://orcid.org/0009-0007-7754-8153
  - family-names: Wu
    given-names: Yuesong
  - family-names: Chen
    given-names: Bin
    orcid: https://orcid.org/0000-0001-8858-874X
  - family-names: Cui
    given-names: Yuehua
title: "STANCE: a unified statistical model to detect cell-type-specific spatially variable genes in spatial transcriptomics"
version: 1.0.0
identifiers:
  - type: doi
    value: 10.5281/zenodo.14768010
date-released: 2025-01-29

GitHub Events

Total
  • Create event: 1
  • Issues event: 6
  • Release event: 1
  • Watch event: 5
  • Issue comment event: 8
  • Push event: 8
  • Pull request event: 2
  • Fork event: 2
Last Year
  • Create event: 1
  • Issues event: 6
  • Release event: 1
  • Watch event: 5
  • Issue comment event: 8
  • Push event: 8
  • Pull request event: 2
  • Fork event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 4
  • Total pull requests: 1
  • Average time to close issues: 1 day
  • Average time to close pull requests: 19 minutes
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 1
  • Average time to close issues: 1 day
  • Average time to close pull requests: 19 minutes
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • Yaohui2000 (2)
  • hanbyul-lee (1)
  • shippp-zz (1)
Pull Request Authors
  • Yaohui2000 (1)
Top Labels
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Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • KRLS >= 1.0 imports
  • RColorBrewer * imports
  • Rcpp * imports
  • RcppArmadillo * imports
  • SPARK >= 1.1.1 imports
  • gaston * imports
  • ggplot2 * imports
  • grDevices * imports
  • methods * imports
  • parallel * imports
  • reshape2 * imports
  • stats * imports