Research graph
References from Quantifying distribution shifts in single-cell data with scXMatch. Local targets link to admitted publications; unresolved targets remain external evidence.
Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction
10.1038/s41467-019-12054-3 · 2019 · External reference
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10.1145/335191.335388 · 2000 · External reference
The specious art of single-cell genomics
10.1371/journal.pcbi.1011288 · 2023 · External reference
Stimulation via the CD3 and CD28 molecules induces responsiveness to IL-4 in CD4 + CD29 + CD45R-memory T lymphocytes
10.4049/jimmunol.143.6.1761 · 1989 · External reference
Significance analysis for clustering with single-cell RNA-sequencing data
10.1038/s41592-023-01933-9 · 2023 · External reference
Bioconda: sustainable and comprehensive software distribution for the life sciences
10.1038/s41592-018-0046-7 · 2018 · External reference
Unresolved reference
2024 · External reference
Pertpy: an end-to-end framework for perturbation analysis
10.1038/s41592-025-02909-7 · 2026 · External reference
10.1101/2023.12.26.572833
10.1101/2023.12.26.572833 · 2023 · External reference
Development of a high-throughput pipeline to characterize microglia morphological states at a single-cell resolution
10.1523/eneuro.0014-24.2024 · 2024 · External reference
Method of moments framework for differential expression analysis of single-cell RNA sequencing data
10.1016/j.cell.2024.09.044 · 2024 · External reference
A critical assessment of clustering algorithms to improve cell clustering and identification in single-cell transcriptome study
10.1093/bib/bbad497 · 2023 · External reference
The molecular signatures database (MSigDB) hallmark gene set collection
10.1016/j.cels.2015.12.004 · 2015 · External reference
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
10.1186/s13059-014-0550-8 · 2014 · External reference
Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action
10.1038/s41467-020-17440-w · 2020 · External reference
10.48550/arxiv.1802.03426
10.48550/arxiv.1802.03426 · 2018 · External reference
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
10.1038/s41587-021-00927-2 · 2021 · External reference
Exploring genetic interaction manifolds constructed from rich single-cell phenotypes
10.1126/science.aax4438 · 2019 · External reference
A new look at T cell receptor signaling to nuclear factor-κB
10.1016/j.it.2013.02.002 · 2013 · External reference
scPerturb: harmonized single-cell perturbation data
10.1038/s41592-023-02144-y · 2024 · External reference
Unresolved reference
External reference
edgeR: a bioconductor package for differential expression analysis of digital gene expression data
10.1093/bioinformatics/btp616 · 2010 · External reference
An exact distribution-free test comparing two multivariate distributions based on adjacency
10.1111/j.1467-9868.2005.00513.x · 2005 · External reference
Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming
10.1016/j.cell.2019.01.006 · 2019 · External reference
Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo
10.1371/journal.pcbi.1011859 · 2025 · External reference
T cell receptor (TCR) signaling in health and disease
10.1038/s41392-021-00823-w · 2021 · External reference
Cell type prioritization in single-cell data
10.1038/s41587-020-0605-1 · 2021 · External reference
Bias, robustness and scalability in single-cell differential expression analysis
10.1038/nmeth.4612 · 2018 · External reference
Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses
10.1101/2023.07.21.550107 · 2024 · External reference
Confronting false discoveries in single-cell differential expression
10.1038/s41467-021-25960-2 · 2021 · External reference
Non-canonical NF-κB signaling pathway
10.1038/cr.2010.177 · 2011 · External reference
The non-canonical NF-κB pathway in immunity and inflammation
10.1038/nri.2017.52 · 2017 · External reference
Resident macrophages cloak tissue microlesions to prevent neutrophil-driven inflammatory damage
10.1016/j.cell.2019.02.028 · 2019 · External reference
Visualizing data using t-SNE
2008 · External reference
The scverse project provides a computational ecosystem for single-cell omics data analysis
10.1038/s41587-023-01733-8 · 2023 · External reference
anndata: access and store annotated data matrices
10.21105/joss.04371 · 2024 · External reference
10.1007/978-1-4612-4380-9_16
10.1007/978-1-4612-4380-9_16 · 1992 · External reference
SCANPY: large-scale single-cell gene expression data analysis
10.1186/s13059-017-1382-0 · 2018 · External reference
Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data
10.1186/s13059-022-02622-0 · 2022 · External reference
Shape descriptors of the “never resting” microglia in three different acute brain injury models in mice
10.1186/s40635-015-0039-0 · 2015 · External reference
Splatter: simulation of single-cell RNA sequencing data
10.1186/s13059-017-1305-0 · 2017 · External reference
