Integrating single-cell transcriptomic data across different conditions, technologies, and species

A Butler, P Hoffman, P Smibert, E Papalexi… - Nature …, 2018 - nature.com
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied
to experiments representing a single condition, technology, or species to discover and …

Identifying cell types to interpret scRNA-seq data: how, why and more possibilities

Z Wang, H Ding, Q Zou - Briefings in functional genomics, 2020 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has generated numerous data and renewed our
understanding of biological phenomena at the cellular scale. Identification of cell types has …

ClusterMap: comparing analyses across multiple single cell RNA-seq profiles

X Gao, D Hu, M Gogol, H Li - bioRxiv, 2018 - biorxiv.org
Single cell RNA-Seq facilitates the characterization of cell type heterogeneity and
developmental processes. Further study of single cell profiles across different conditions …

Scanorama: integrating large and diverse single-cell transcriptomic datasets

BL Hie, S Kim, TA Rando, B Bryson, B Berger - Nature Protocols, 2024 - nature.com
Merging diverse single-cell RNA sequencing (scRNA-seq) data from numerous
experiments, laboratories and technologies can uncover important biological insights …

Panoramic stitching of heterogeneous single-cell transcriptomic data

B Hie, B Bryson, B Berger - BioRxiv, 2018 - biorxiv.org
Researchers are generating single-cell RNA sequencing (scRNA-seq) profiles of diverse
biological systems–and every cell type in the human body. Leveraging this data to gain …

scID: identification of transcriptionally equivalent cell populations across single cell RNA-seq data using discriminant analysis

K Boufea, S Seth, NN Batada - BioRxiv, 2018 - biorxiv.org
The power of single cell RNA sequencing (scRNA-seq) stems from its ability to uncover cell
type-dependent phenotypes, which rests on the accuracy of cell type identification. However …

Multi-level cellular and functional annotation of single-cell transcriptomes

N Mikolajewicz, KR Brown, J Moffat, H Han - Biorxiv, 2022 - biorxiv.org
Single-cell RNA-sequencing (scRNA-seq) offers unprecedented insight into heterogenous
biology, allowing for the interrogation of cellular populations and gene expression programs …

Addressing the looming identity crisis in single cell RNA-seq

M Crow, A Paul, S Ballouz, ZJ Huang, J Gillis - bioRxiv, 2017 - biorxiv.org
Single cell RNA-sequencing technology (scRNA-seq) provides a new avenue to discover
and characterize cell types, but the experiment-specific technical biases and analytic …

scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication

Y Lin, S Ghazanfar, K Wang, JA Gagnon-Bartsch… - bioRxiv, 2018 - biorxiv.org
Concerted examination of multiple collections of single cell RNA-Seq (scRNA-Seq) data
promises further biological insights that cannot be uncovered with individual datasets …

Scaling up single-cell RNA-seq data analysis with CellBridge workflow

N Nouri, AH Kurlovs, G Gaglia, E de Rinaldis… - …, 2023 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression
at the individual cell level, unraveling unprecedented insights into cellular heterogeneity …