Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data

D Feng, CE Whitehurst, D Shan, JD Hill, YG Yue - BMC genomics, 2019 - Springer
Background Single cell transcriptome sequencing has become an increasingly valuable
technology for dissecting complex biology at a resolution impossible with bulk sequencing …

CellView: interactive exploration of high dimensional single cell RNA-seq data

MT Bolisetty, ML Stitzel, P Robson - bioRxiv, 2017 - biorxiv.org
Advances in high-throughput single cell transcriptomics technologies have revolutionized
the study of complex tissues. It is now possible to measure gene expression across …

ShIVA: a user-friendly and interactive interface giving biologists control over their single-cell RNA-seq data

R Aussel, M Asif, S Chenag, S Jaeger, P Milpied… - Scientific Reports, 2023 - nature.com
Single-cell technologies have revolutionised biological research and applications. As they
continue to evolve with multi-omics and spatial resolution, analysing single-cell datasets is …

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 …

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

CK Mah, AT Wenzel, EF Juarez, T Tabor… - …, 2019 - pmc.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 …

Current best practices in single‐cell RNA‐seq analysis: a tutorial

MD Luecken, FJ Theis - Molecular systems biology, 2019 - embopress.org
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …

scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies

KT Schmid, B Höllbacher, C Cruceanu… - Nature …, 2021 - nature.com
Single cell RNA-seq has revolutionized transcriptomics by providing cell type resolution for
differential gene expression and expression quantitative trait loci (eQTL) analyses. However …

Practical Considerations for Single‐Cell Genomics

C Regan, J Preall - Current protocols, 2022 - Wiley Online Library
The single‐cell revolution in the field of genomics is in full bloom, with clever new molecular
biology tricks appearing regularly that allow researchers to explore new modalities or scale …

Experimental considerations for single-cell RNA sequencing approaches

QH Nguyen, N Pervolarakis, K Nee… - Frontiers in cell and …, 2018 - frontiersin.org
Single-cell transcriptomic technologies have emerged as powerful tools to explore cellular
heterogeneity at the resolution of individual cells. Previous scientific knowledge in cell …

CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods

S Su, L Tian, X Dong, PF Hickey, S Freytag… - …, 2020 - academic.oup.com
Motivation Bioinformatic analysis of single-cell gene expression data is a rapidly evolving
field. Hundreds of bespoke methods have been developed in the past few years to deal with …