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Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution



scLINE: A multi-network integration framework based on network embedding for representation of single-cell RNA-seq data.



Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space


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10.1186/s13059-021-02422-y

Enabling reproducible re-analysis of single-cell data



Variability in scRNA-Seq analysis is mitigated by regularized or supervised approaches



SCMAG: A Semisupervised Single-Cell Clustering Method Based on Matrix Aggregation Graph Convolutional Neural Network


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10.1371/journal.pcbi.1009290

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data


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10.1371/journal.pcbi.1008804

JSOM: Jointly-evolving self-organizing maps for alignment of biological datasets and identification of related clusters



MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution



Single-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations


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10.1093/bioinformatics/btab426

scAMACE: Model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation.


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10.1093/bioinformatics/btab260

RVAgene: generative modeling of gene expression time series data



scAMACE: Model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation



Axes of inter-sample variability among transcriptional neighborhoods reveal disease-associated cell states in single-cell data



Unsupervised weights selection for optimal transport based dataset integration



Algorithmic Reconstruction of GBM Network Complexity



CDCP: a visualization and analyzing platform for single-cell datasets



Inferring relevant tissues and cell types for complex traits in genome-wide association studies



scvi-tools: a library for deep probabilistic analysis of single-cell omics data



A single-cell reference atlas delineates CD4+ T cell subtype-specific adaptation during acute and chronic viral infections



Connectome: computation and visualization of cell-cell signaling topologies in single-cell systems data



Bioinformatics analysis of the role of CXC ligands in the microenvironment of head and neck tumor



Accurate single-cell genotyping utilizing information from the local genome territory



ScCAEs: deep clustering of single-cell RNA-seq via convolutional autoencoder embedding and soft K-means.



A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation.



Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system



EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies.


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10.1038/s41587-021-00867-x

Iterative single-cell multi-omic integration using online learning



SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues



Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways



Detection of Hematopoietic Stem Cell Transcriptome in Human Fetal Kidneys and Kidney Organoids Derived From Human Induced Pluripotent Stem Cells



MOSCATO: A Supervised Approach for Analyzing Multi-Omic Single-Cell Data


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10.1093/bioinformatics/btab594

Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona.



Detection of hematopoietic stem cell transcriptome in human fetal kidneys and kidney organoids derived from human induced pluripotent stem cells (iPSC)


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10.2174/1574893616666210528164302

Ensemble Adaptive Total Variation Graph Regularized NMF for Single-cell RNA-Seq Data Analysis


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10.1093/bioinformatics/btab503

UCSC Cell Browser: Visualize Your Single-Cell Data.


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10.1038/s41587-021-00989-2

Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA).



High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0


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10.1038/s41467-021-21515-7

Spatially mapped single-cell chromatin accessibility



Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing



miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data


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10.1016/j.csbj.2021.06.043

UCell: Robust and scalable single-cell gene signature scoring


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10.1016/j.ydbio.2021.08.001

Single-cell transcriptomics in the Drosophila visual system: Advances and perspectives on cell identity regulation, connectivity, and neuronal diversity evolution.



UCell: robust and scalable single-cell gene signature scoring



scMethBank: a database for single-cell whole genome DNA methylation maps.



Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq



Integrating single-cell datasets with ambiguous batch information by incorporating molecular network features.



DTFLOW: Inference and Visualization of Single-cell Pseudotime Trajectory Using Diffusion Propagation.



Robust and annotation-free analysis of alternative splicing across diverse cell types in mice


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10.1038/s41587-021-01066-4

Co-varying neighborhood analysis identifies cell populations associated with phenotypes of interest from single-cell transcriptomics.


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10.1186/s12864-020-07300-8

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™



Nonnegative matrix factorization integrates single-cell multi-omic datasets with partially overlapping features


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10.1038/s41587-021-01033-z

Differential abundance testing on single-cell data using k-nearest neighbor graphs.



Maximizing Statistical Power to Detect Differentially Abundant Cell States With scPOST


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