Browse Articles

Enhanced recognition and counting of high-coverage Amorphophallus konjac by integrating UAV RGB imagery and deep learning

High H2O2 production in membrane-free electrolyzer via anodic bubble shielding towards robust rural disinfection

Virulence factors of Pseudomonas aeruginosa and immune response during exacerbations and stable phase in bronchiectasis

Achieving burst Li+ channels via quasi-two-dimensional fluorinated metal-organic framework modulating functionalized interface

Uncovering pre-cytokinetic block in cancer cells under shear stress using a disturbed flow-generating device

Engineering nanozyme immunomodulator with magnetic targeting effect for cascade-enzyodynamic and ultrasound-reinforced metallo-immunotherapy in prostate carcinoma

Loose circle and rock mass strength tests of extremely thin layered surrounding rock in large deformation tunnels

Polymorphic relaxor phase and defect dipole polarization co-reinforced capacitor energy storage in temperature-monitorable high-entropy ferroelectrics

Determining whether a phosphatic concretion containing a Cretaceous juvenile crocodylian is a coprolite or a non-fecal concretion

Cooperation of TRADD- and RIPK1-dependent cell death pathways in maintaining intestinal homeostasis

Influence of blade installation angle spanwise distribution on the energy characteristics of mining contra-rotating axial flow fan

Thermal biasing for lattice symmetry breaking and topological edge state imaging

Building rooftop extraction from high resolution aerial images using multiscale global perceptron with spatial context refinement

Rational design of precatalysts and controlled evolution of catalyst-electrolyte interface for efficient hydrogen production

Preliminary study demonstrating cancer cells detection at the margins of whole glioblastoma specimens with Raman spectroscopy imaging

A randomised controlled non-inferiority trial to compare the efficacy of ‘HPV screen, triage and treat’ with ‘HPV screen and treat’ approach for cervical cancer prevention among women living with HIV

Melanin from the fungus Gliocephalotrichum simplex protects seeds from the effects of exposure to gamma radiation

Non-invasive in vivo monitoring of PROTAC-mediated protein degradation using an environment-sensitive reporter

An intelligent prediction method for rock core integrity based on deep learning

Interpretable single-cell factor decomposition using sciRED

Abstract Single-cell RNA sequencing maps gene expression heterogeneity within a tissue. However, identifying biological signals in this data is challenging due to confounding technical factors, sparsity, and high dimensionality. Data factorization methods address this by separating and identifying signals in the data, such as gene expression programs, but the resulting factors must be manually interpreted. We developed Single-Cell Interpretable REsidual Decomposition (sciRED) to improve the interpretation of scRNA-seq factor analysis. sciRED removes known confounding effects, uses rotations to improve factor interpretability, maps factors to known covariates, identifies unexplained factors that may capture hidden biological phenomena, and determines the genes and biological processes represented by the resulting factors. We apply sciRED to multiple scRNA-seq datasets and identify sex-specific variation in a kidney map, discern strong and weak immune stimulation signals in a PBMC dataset, reduce ambient RNA contamination in a rat liver atlas to help identify strain variation and reveal rare cell type signatures and anatomical zonation gene programs in a healthy human liver map. These demonstrate that sciRED is useful in characterizing diverse biological signals within scRNA-seq data.