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 …

Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis

SU Umu, K Rapp Vander-Elst, VT Karlsen… - …, 2023 - academic.oup.com
Background Single-cell RNA sequencing (scRNA-seq) provides high-resolution
transcriptome data to understand the heterogeneity of cell populations at the single-cell …

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 …

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 …

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

P Moreno, N Huang, JR Manning, S Mohammed… - Nature …, 2021 - nature.com
To the Editor—As single-cell RNA sequencing (scRNA-seq) becomes widespread,
accessible and scalable computational pipelines for data analysis are needed. We introduce …

scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis

JJ Cai - 2020 - academic.oup.com
Motivation Single-cell RNA sequencing (scRNA-seq) technology has revolutionized the way
research is done in biomedical sciences. It provides an unprecedented level of resolution …

WASP: a versatile, web-accessible single cell RNA-Seq processing platform

A Hoek, K Maibach, E Özmen, AI Vazquez-Armendariz… - BMC genomics, 2021 - Springer
Background The technology of single cell RNA sequencing (scRNA-seq) has gained
massively in popularity as it allows unprecedented insights into cellular heterogeneity as …

[HTML][HTML] Practical bioinformatics pipelines for single-cell RNA-seq data analysis

J He, L Lin, J Chen - Biophysics Reports, 2022 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool to explore cells. With an
increasing number of scRNA-seq data analysis tools that have been developed, it is …

SingleCAnalyzer: interactive analysis of single cell RNA-Seq data on the cloud

C Prieto, D Barrios, A Villaverde - Frontiers in bioinformatics, 2022 - frontiersin.org
Single-cell RNA sequencing (scRNA-Seq) enables researchers to quantify the
transcriptomes of individual cells. The capacity of researchers to perform this type of analysis …

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 …