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 …

Cerebro: interactive visualization of scRNA-seq data

R Hillje, PG Pelicci, L Luzi - Bioinformatics, 2020 - academic.oup.com
Despite the growing availability of sophisticated bioinformatic methods for the analysis of
single-cell RNA-seq data, few tools exist that allow biologists without extensive bioinformatic …

dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit

DG Bunis, J Andrews, GK Fragiadakis, TD Burt… - …, 2020 - academic.oup.com
A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is
color blindness-friendly by default, robustly documented to power ease-of-use and allows …

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

DJ McCarthy, KR Campbell, ATL Lun, QF Wills - Bioinformatics, 2017 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) is increasingly used to study gene
expression at the level of individual cells. However, preparing raw sequence data for further …

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

V Gardeux, FPA David, A Shajkofci, PC Schwalie… - …, 2017 - academic.oup.com
Motivation Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of
thousands of individual cells, enabling the molecular exploration of tissues at the cellular …

ascend: R package for analysis of single-cell RNA-seq data

A Senabouth, SW Lukowski, JA Hernandez… - …, 2019 - academic.oup.com
Background Recent developments in single-cell RNA sequencing (scRNA-seq) platforms
have vastly increased the number of cells typically assayed in an experiment. Analysis of …

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data

Z Wang, J Hu, WE Johnson, JD Campbell - BMC bioinformatics, 2019 - Springer
Background Single-cell RNA sequencing (scRNA-seq) enables the high-throughput
quantification of transcriptional profiles in single cells. In contrast to bulk RNA-seq, additional …

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 …

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

X Zhu, TK Wolfgruber, A Tasato, C Arisdakessian… - Genome medicine, 2017 - Springer
Background Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform
to study heterogeneity at the single-cell level. Computational methods to process scRNA …

Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2. 0

A Jiang, L You, RG Snell… - NAR Genomics and …, 2023 - academic.oup.com
Complex biological traits and disease often involve patterns of gene expression that can be
characterised and examined. Here we present ICARUS v2. 0, an update to our single cell …