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 …

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

E Mereu, A Lafzi, C Moutinho, C Ziegenhain… - Nature …, 2020 - nature.com
Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the
transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands …

Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments

G Ebrahimi, B Orabi, M Robinson, C Chauve… - Iscience, 2022 - cell.com
Single-cell RNA sequencing allows for characterizing the gene expression landscape at the
cell type level. However, because of its use of short-reads, it is severely limited at detecting …

Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape

L Zappia, FJ Theis - Genome biology, 2021 - Springer
Recent years have seen a revolution in single-cell RNA-sequencing (scRNA-seq)
technologies, datasets, and analysis methods. Since 2016, the scRNA-tools database has …

FIRM: Flexible integration of single-cell RNA-sequencing data for large-scale multi-tissue cell atlas datasets

J Ming, Z Lin, J Zhao, X Wan… - Briefings in …, 2022 - academic.oup.com
Single-cell RNA-sequencing (scRNA-seq) is being used extensively to measure the mRNA
expression of individual cells from deconstructed tissues, organs and even entire organisms …

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

JW Bagnoli, C Ziegenhain, A Janjic, LE Wange… - Nature …, 2018 - nature.com
Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method
to characterize cellular identities and processes. Consequently, improving its sensitivity …

Introduction to single‐cell RNA sequencing

TK Olsen, N Baryawno - Current protocols in molecular biology, 2018 - Wiley Online Library
During the last decade, high‐throughput sequencing methods have revolutionized the entire
field of biology. The opportunity to study entire transcriptomes in great detail using RNA …

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries

KA Riemondy, M Ransom, C Alderman… - Nucleic acids …, 2019 - academic.oup.com
Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression
profiles for thousands of single cells in a single experiment. The information in these profiles …

ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells

A Jiang, RG Snell, K Lehnert - Bioinformatics, 2024 - academic.oup.com
Motivation In recent years, improvements in throughput of single cell RNA-seq have resulted
in a significant increase in the number of cells profiled. The generation of single cell RNA …

Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE

Y You, YDJ Prawer, R De Paoli-Iseppi, CPJ Hunt… - Genome Biology, 2023 - Springer
Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification of RNA
isoforms in individual cells. However, long-read scRNA-seq using the Oxford Nanopore …