ArticleGenomics, proteomics & bioinformatics2021
scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data.
Article in Genomics, proteomics & bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 2 of them syntheses that pooled it.
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Who cites it
32 citing papers in PubMed, 2 syntheses or guidelines pooled it, 46 citations in OpenAlex.
- Variable expression ofProceedings of the National Academy of Sciences of the United States of America · 2024Pooled it
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- A hybrid transcriptome assembly reveals coding and noncoding landscapes in Drosophila hemocytes.Genetics · 2026Article
- A unified framework for selecting and evaluating cell-type-specific gene co-expressions in single-cell data.Briefings in bioinformatics · 2026Article
- Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression.Nature communications · 2026Article
- LncCE: Landscape of Cellularly-elevated lncRNAs in Single Cells Across Normal and Cancer Tissues.Genomics, proteomics & bioinformatics · 2025Article
- scCOSMIX: A Mixed-Effects Framework for Differential Coexpression and Transcriptional Interactions Modeling in Single-Cell RNA-Seq.Statistics in medicine · 2025Article
- Inference of gene coexpression networks from single-cell transcriptome data based on variance decomposition analysis.Briefings in bioinformatics · 2025Article
- Single-cell transcriptome analysis reveals abnormal angiogenesis and placentation by loss of imprinted glutaminyl-peptide cyclotransferase.Journal of Zhejiang University. Science. B · 2025Article
- GSNCASCR: An R Package to Identify Differentially Co-Expressed Curated Gene Sets with Single-Cell RNA-Seq Data.International journal of molecular sciences · 2025Article
- ACT2.6: Global Gene Coexpression Network inGenes · 2025Article
- A single-cell atlas of the Culex tarsalis midgut during West Nile virus infection.PLoS pathogens · 2025Article
- Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay.Genome research · 2024Article
- A statistical approach for systematic identification of transition cells from scRNA-seq data.Cell reports methods · 2024Article
- A single-cell atlas of thebioRxiv : the preprint server for biology · 2024Article
- Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data.BMC bioinformatics · 2024Article
- SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer.Cell reports methods · 2024Article
- Brooklyn plots to identify co-expression dysregulation in single cell sequencing.NAR genomics and bioinformatics · 2024Article
- FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.Bioinformatics (Oxford, England) · 2024Article
- scDiffCoAM: A complete framework to identify potential biomarkers for esophageal squamous cell carcinoma using scRNA-Seq data analysis.Journal of biosciences · 2024Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A system-level understanding of the regulation and coordination mechanisms of gene expression is essential for studying the complexity of biological processes in health and disease. With the rapid development of single-cell RNA sequencing technologies, it is now possible to investigate gene interactions in a cell type-specific manner. Here we propose the scLink method, which uses statistical network modeling to understand the co-expression relationships among genes and construct sparse gene co-expression networks from single-cell gene expression data. We use both simulation and real data studies to demonstrate the advantages of scLink and its ability to improve single-cell gene network analysis. The scLink R package is available at https://github.com/Vivianstats/scLink.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.