» Articles » PMID: 33782609

User-friendly, Scalable Tools and Workflows for Single-cell RNA-seq Analysis

Citing Articles

Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq.

Goclowski C, Jakiela J, Collins T, Hiltemann S, Howells M, Loach M Gigascience. 2025; 14.

PMID: 39775842 PMC: 11707610. DOI: 10.1093/gigascience/giae107.


TME-NET: an interpretable deep neural network for predicting pan-cancer immune checkpoint inhibitor responses.

Ding X, Zhang L, Fan M, Li L Brief Bioinform. 2024; 25(5).

PMID: 39167797 PMC: 11337220. DOI: 10.1093/bib/bbae410.


Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis.

Curion F, Rich-Griffin C, Agarwal D, Ouologuem S, Rue-Albrecht K, May L Genome Biol. 2024; 25(1):181.

PMID: 38978088 PMC: 11229213. DOI: 10.1186/s13059-024-03322-7.


ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists.

Sethi R, Ang K, Li M, Long Y, Ling J, Chen J Nat Commun. 2024; 15(1):5600.

PMID: 38961061 PMC: 11222513. DOI: 10.1038/s41467-024-48188-2.


Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis.

Pan L, Mou T, Huang Y, Hong W, Yu M, Li X Mol Biol Evol. 2023; 40(12).

PMID: 38091963 PMC: 10752348. DOI: 10.1093/molbev/msad267.


References
1.
McCarthy D, Campbell K, Lun A, Wills Q . Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics. 2017; 33(8):1179-1186. PMC: 5408845. DOI: 10.1093/bioinformatics/btw777. View