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 …

[PDF][PDF] Utility of transcriptome sequencing for phylogenetic inference and character evolution

J Wen, AN Egan, RB Dikow… - … -generation sequencing in …, 2015 - repository.si.edu
Transcriptome sequencing or RNA-Seq is one of the most efficient and cost-effective
methods currently available for gene discovery in non-model organisms. Recent studies …

CellFishing. jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

K Sato, K Tsuyuzaki, K Shimizu, I Nikaido - Genome biology, 2019 - Springer
Recent technical improvements in single-cell RNA sequencing (scRNA-seq) have enabled
massively parallel profiling of transcriptomes, thereby promoting large-scale studies …

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

M Crow, A Paul, S Ballouz, ZJ Huang, J Gillis - Nature communications, 2018 - nature.com
Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover
and characterize cell types; however, the experiment-specific technical biases and analytic …

ICARUS, an interactive web server for single cell RNA-seq analysis

A Jiang, K Lehnert, L You, RG Snell - Nucleic acids research, 2022 - academic.oup.com
Here we present ICARUS, a web server to enable users without experience in R to
undertake single cell RNA-seq analysis. The focal point of ICARUS is its intuitive tutorial …

Benchmarking strategies for cross-species integration of single-cell RNA sequencing data

Y Song, Z Miao, A Brazma, I Papatheodorou - Nature Communications, 2023 - nature.com
The growing number of available single-cell gene expression datasets from different species
creates opportunities to explore evolutionary relationships between cell types across …

[HTML][HTML] Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development

DJ Anderson, FM Pauler, A McKenna, J Shendure… - Cell systems, 2022 - cell.com
Mutations are acquired frequently, such that each cell's genome inscribes its history of cell
divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH …

Profiling of single‐cell transcriptomes

W Chen, V Gardeux, A Meireles‐Filho… - Current protocols in …, 2017 - Wiley Online Library
Complex biological systems are composed of multiple cell types whose transcriptional
activity can vary due to differences in cell state, environmental stimulation, or intrinsic …

A review of single-cell RNA-Seq annotation, integration, and cell–cell communication

C Cheng, W Chen, H Jin, X Chen - Cells, 2023 - mdpi.com
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating
cellular biology at an unprecedented resolution, enabling the characterization of cellular …

Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila

SE Mohr, SG Tattikota, J Xu, J Zirin, Y Hu, N Perrimon - Genetics, 2021 - academic.oup.com
Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify
clusters of cells that share common gene expression signatures. A major challenge in …