[HTML][HTML] An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data

CK Mah, AT Wenzel, EF Juarez, T Tabor… - …, 2018 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) has emerged as a popular method to profile gene
expression at the resolution of individual cells. While there have been methods and software …

Cell-level metadata are indispensable for documenting single-cell sequencing datasets

S Puntambekar, JR Hesselberth, KA Riemondy… - PLoS Biology, 2021 - journals.plos.org
Single-cell RNA sequencing (scRNA-seq) provides an unprecedented view of cellular
diversity of biological systems. However, across the thousands of publications and datasets …

Developmental scRNAseq trajectories in gene-and cell-state space—The flatworm example

M Schmidt, H Loeffler-Wirth, H Binder - Genes, 2020 - mdpi.com
Single-cell RNA sequencing has become a standard technique to characterize tissue
development. Hereby, cross-sectional snapshots of the diversity of cell transcriptomes were …

High-throughput single-cell RNA sequencing and data analysis

null Sagar, JS Herman, JA Pospisilik… - CpG Islands: Methods and …, 2018 - Springer
Understanding biological systems at a single cell resolution may reveal several novel
insights which remain masked by the conventional population-based techniques providing …

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

H Dueck, M Khaladkar, TK Kim, JM Spaethling… - Genome biology, 2015 - Springer
Background Differentiation of metazoan cells requires execution of different gene
expression programs but recent single-cell transcriptome profiling has revealed …

The cell as a bag of RNA

SR Quake - Trends in Genetics, 2021 - cell.com
Genomic sequencing has provided insight into the genetic characterization of many
organisms, and we are now seeing sequencing technologies turned towards phenotypic …

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity

Y Sun, WJ Shim, S Shen, E Sinniah… - Nucleic Acids …, 2023 - academic.oup.com
Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-
seq) data are essential for biological interpretation of cell processes. Here, we present …

Single‐cell sequencing methodologies: from transcriptome to multi‐dimensional measurement

Y Chen, J Song, Q Ruan, X Zeng, L Wu, L Cai… - Small …, 2021 - Wiley Online Library
Cells are the basic building blocks of biological systems, with inherent unique molecular
features and development trajectories. The study of single cells facilitates in‐depth …

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

L Zappia, B Phipson, A Oshlack - PLoS computational biology, 2018 - journals.plos.org
As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the
number of tools designed to analyse these data has dramatically increased. Navigating the …

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA‐seq experiments

N Vijay, JW Poelstra, A Künstner… - Molecular ecology, 2013 - Wiley Online Library
Transcriptome S hotgun S equencing (RNA‐seq) has been readily embraced by geneticists
and molecular ecologists alike. As with all high‐throughput technologies, it is critical to …