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Detection of differentially abundant cell subpopulations discriminates biological states in scRNA-seq data

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
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Comprehensive Integration of Single-Cell Data
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Nap1l1 Controls Embryonic Neural Progenitor Cell Proliferation and Differentiation in the Developing Brain
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Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin
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CD63 associates with CD11/CD18 in large detergent‐resistant complexes after translocation to the cell surface in human neutrophils1
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Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
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Integrating single-cell transcriptomic data across different conditions, technologies, and species
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Massively parallel digital transcriptional profiling of single cells
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SOCS3 negatively regulates IL-6 signaling in vivo
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IL-6 induces an anti-inflammatory response in the absence of SOCS3 in macrophages
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Testing for differential abundance in mass cytometry data
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Single-cell RNA-seq denoising using a deep count autoencoder
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Quantifying the effect of experimental perturbations at single-cell resolution
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COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis
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Cell type prioritization in single-cell data
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Locally instructed CXCR4hi neutrophils trigger environment-driven allergic asthma through the release of neutrophil extracellular traps
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Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19
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SAVER: gene expression recovery for single-cell RNA sequencing
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Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data
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Single-cell transcriptomic profiling of the aging mouse brain
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The transcription factor MafB promotes anti-inflammatory M2 polarization and cholesterol efflux in macrophages
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Neutrophil Dysfunction in the Airways of Children with Acute Respiratory Failure Due to Lower Respiratory Tract Viral and Bacterial Coinfections
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Transgenic Aedes aegypti Mosquitoes Transfer Genes into a Natural Population
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Interleukin 1 receptor antagonist mediates the antiinflammatory and antifibrotic effect of mesenchymal stem cells during lung injury
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Conditional Vascular Cell Adhesion Molecule 1 Deletion in Mice
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EXPLOITING LOW-DIMENSIONAL STRUCTURE IN ASTRONOMICAL SPECTRA
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Robust classification of single-cell transcriptome data by nonnegative matrix factorization
inferredcites →https://doi.org/10.1093/bioinformatics/btx196openalex-snapshot
Removal of batch effects using distribution-matching residual networks
inferredcites →https://doi.org/10.1093/bioinformatics/btz024openalex-snapshot
ClusterMap: compare multiple single cell RNA-Seq datasets across different experimental conditions
inferredcites →https://doi.org/10.1093/mnras/stx1807openalex-snapshot
Local two-sample testing: a new tool for analysing high-dimensional astronomical data
inferredcites →https://doi.org/10.1101/331330openalex-snapshot
ClusterMap: Comparing analyses across multiple Single Cell RNA-Seq profiles
inferredcites →https://doi.org/10.1101/397588openalex-snapshot
Zero-preserving imputation of scRNA-seq data using low-rank approximation
inferredcites →https://doi.org/10.1101/655365openalex-snapshot
Accurate denoising of single-cell RNA-Seq data using unbiased principal component analysis
inferredcites →https://doi.org/10.1109/dsaa.2015.7344835openalex-snapshot
Beyond two-sample-tests: Localizing data discrepancies in high-dimensional spaces
inferredcites →https://doi.org/10.1109/tit.2012.2227680openalex-snapshot
How Correlations Influence Lasso Prediction
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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Regression Shrinkage and Selection Via the Lasso
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Misguided drug advice for COVID-19
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Multidimensional binary search trees used for associative searching
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Ectopic Expression of Vascular Cell Adhesion Molecule-1 as a New Mechanism for Tumor Immune Evasion
inferredcites →https://doi.org/10.1158/0008-5472.can-07-1543openalex-snapshot
The Role of Vascular Cell Adhesion Molecule-1 in Tumor Immune Evasion
inferredcites →https://doi.org/10.1164/rccm.201712-2410ocopenalex-snapshot
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis
inferredcites →https://doi.org/10.1182/blood-2006-04-015164openalex-snapshot
Expression of LAG-3 by tumor-infiltrating lymphocytes is coincident with the suppression of latent membrane antigen–specific CD8+ T-cell function in Hodgkin lymphoma patients
inferredcites →https://doi.org/10.1182/blood-2012-06-436212openalex-snapshot
Genetic programs expressed in resting and IL-4 alternatively activated mouse and human macrophages: similarities and differences
inferredcites →https://doi.org/10.1184/r1/6586613.v1openalex-snapshot
Exploiting Low-Dimensional Structure in Astronomical Spectra
inferredcites →https://doi.org/10.1186/s12859-019-3211-9openalex-snapshot
scDC: single cell differential composition analysis
inferredcites →https://doi.org/10.1186/s13059-019-1795-zopenalex-snapshot
A comparison of automatic cell identification methods for single-cell RNA sequencing data
inferredcites →https://doi.org/10.1214/19-ejs1648openalex-snapshot
Global and local two-sample tests via regression
inferredcites →https://doi.org/10.3389/fimmu.2014.00058openalex-snapshot
SOCS3, a Major Regulator of Infection and Inflammation
inferredcites →https://doi.org/10.3389/fimmu.2019.01078openalex-snapshot
Cell Adhesion Molecules and Their Roles and Regulation in the Immune and Tumor Microenvironment
inferredcites →https://doi.org/10.3390/genes10020098openalex-snapshot
A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data
inferredcites →https://doi.org/10.3390/genes10080611openalex-snapshot
Multi-Objective Optimized Fuzzy Clustering for Detecting Cell Clusters from Single-Cell Expression Profiles
inferredcites →https://doi.org/10.3390/ijms19041057openalex-snapshot
Emerging Roles of Vascular Cell Adhesion Molecule-1 (VCAM-1) in Immunological Disorders and Cancer
inferredcites →https://doi.org/10.4049/jimmunol.1401644openalex-snapshot
OX40- and CD27-Mediated Costimulation Synergizes with Anti–PD-L1 Blockade by Forcing Exhausted CD8+ T Cells To Exit Quiescence
inferredcites →https://doi.org/10.48550/arxiv.1711.04712openalex-snapshot
Randomized Near Neighbor Graphs, Giant Components, and Applications in Data Science
inferredcites →https://doi.org/10.48550/arxiv.1712.09005openalex-snapshot
Efficient Algorithms for t-distributed Stochastic Neighborhood Embedding
inferredcites →https://doi.org/10.48550/arxiv.1810.04247openalex-snapshot
Feature Selection using Stochastic Gates
inferredcites →https://doi.org/10.7287/peerj.preprints.27885v3openalex-snapshot
12 Grand Challenges in Single-Cell Data Science
inferredcites →https://doi.org/10.7717/peerj.2888openalex-snapshot
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-1-0716-4276-4_13openalex-snapshot
Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach
inferred← citeshttps://doi.org/10.1016/j.celrep.2021.109698openalex-snapshot
Transitions in lineage specification and gene regulatory networks in hematopoietic stem/progenitor cells over human development
inferred← citeshttps://doi.org/10.1038/s41467-023-42841-yopenalex-snapshot
A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples
inferred← citeshttps://doi.org/10.1038/s41467-024-44823-0openalex-snapshot
Trajectory inference across multiple conditions with condiments
inferred← citeshttps://doi.org/10.1038/s41587-021-01033-zopenalex-snapshot
Differential abundance testing on single-cell data using k-nearest neighbor graphs
inferred← citeshttps://doi.org/10.1038/s41592-023-02040-5openalex-snapshot
Causal identification of single-cell experimental perturbation effects with CINEMA-OT
inferred← citeshttps://doi.org/10.1101/2021.03.09.433671openalex-snapshot
Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
inferred← citeshttps://doi.org/10.48550/arxiv.2011.03418openalex-snapshot
Local Two-Sample Testing over Graphs and Point-Clouds by Random-Walk Distributions
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