ScRNAbox: empowering single-cell RNA sequencing on high performance computing systems

Abstract Background Single-cell RNA sequencing (scRNAseq) offers powerful insights, but the surge in sample sizes demands more computational power than local workstations can provide. Consequently, high-performance computing (HPC) systems have become imperative. Existing web apps designed to analyze...

Full description

Bibliographic Details
Published in:	BMC Bioinformatics
Main Authors:	Rhalena A. Thomas, Michael R. Fiorini, Saeid Amiri, Edward A. Fon, Sali M. K. Farhan
Format:	Article
Language:	English
Published:	BMC 2024-10-01
Subjects:	Single-cell RNA sequencing ScRNAseq High performance computing systems Pipeline
Online Access:	https://doi.org/10.1186/s12859-024-05935-y

Similar Items

The impact of dropouts in scRNAseq dense neighborhood analysis
by: Alisa Pavel, et al.
Published: (2025-01-01)

Profiling the peripheral immune response to ex vivo TNF stimulation in untreated juvenile idiopathic arthritis using single cell RNA sequencing
by: Kathleen J. Imbach, et al.
Published: (2023-02-01)

Mapping Cell Identity from scRNA-seq: A primer on computational methods
by: Daniele Traversa, et al.
Published: (2025-01-01)

Characterizing Fibroblast Heterogeneity in Diabetic Wounds Through Single-Cell RNA-Sequencing
by: Helen H. Wang, et al.
Published: (2024-11-01)

SC3s: efficient scaling of single cell consensus clustering to millions of cells
by: Fu Xiang Quah, et al.
Published: (2022-12-01)

Integrated analysis of single-cell and bulk RNA-sequencing identifies a signature based on drug response genes to predict prognosis and therapeutic response in ovarian cancer
by: ZhenWei Zhang, et al.
Published: (2024-07-01)

Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation
by: Philip Schmassmann, et al.
Published: (2023-12-01)

Single-cell analysis reveals alternations between the aged and young mice prostates
by: Yang Li, et al.
Published: (2024-10-01)

Meta-Analysis of Human and Mouse Biliary Epithelial Cell Gene Profiles
by: Stefaan Verhulst, et al.
Published: (2019-09-01)

Editorial: Multiomics approaches in the central nervous system and neuropathies
by: Emil Kriukov, et al.
Published: (2025-08-01)

Tany-Seq: Integrated Analysis of the Mouse Tanycyte Transcriptome
by: Andrew I. Sullivan, et al.
Published: (2022-05-01)

Single-cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration
by: Laura Celotto, et al.
Published: (2023-11-01)

Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis
by: Oliver Krenkel, et al.
Published: (2019-05-01)

Single-cell RNA sequencing highlights the influence of innate and adaptive immune response mechanisms in psoriatic arthritis
by: Melanie R. Nielsen, et al.
Published: (2025-02-01)

Where single-cell transcriptomics fails T cells: The misuse of unsupervised clustering for T-cell annotationThis perspective used publicly available data (DOI: 10.5281/zenodo.12569981; ).
by: Kerry A. Mullan, et al.
Published: (2025-12-01)

scRNAseq, bulk-RNAseq and Future Deep Learning RNAseq Analysis: Powerful Prediction Tools in Prostate Cancer Therapy
by: Mohammad Hosein Karimi
Published: (2024-09-01)

Early immune response to Coccidioides is characterized by robust neutrophil and fibrotic macrophage recruitment and differentiation
by: Nadia Miranda, et al.
Published: (2025-09-01)

Epiplakin expression is lost in psoriatic skin lesions and is downregulated by IFN-γ in ex vivo skin cultures
by: Hannes Kühtreiber, et al.
Published: (2025-07-01)

Single-cell analysis reveals significant transcriptomic alterations in preclinical Crohn’s disease
by: Dimitrios Kioroglou, et al.
Published: (2025-05-01)

The Human Early Maternal–Embryonic Interactome
by: Adam Stevens, et al.
Published: (2023-02-01)

Updated single cell reference atlas for the starlet anemone Nematostella vectensis
by: Alison G. Cole, et al.
Published: (2024-03-01)

Single-Cell Transcriptomic Reveals Dual and Multi-Transmitter Use in Neurons Across Metazoans
by: Clarisse Brunet Avalos, et al.
Published: (2021-02-01)

Editorial: Non-neuronal cell heterogeneity in the nervous system during health and disease
by: Greg J. Duncan, et al.
Published: (2022-10-01)

Single-cell RNA sequencing highlights the role of distinct natural killer subsets in sporadic amyotrophic lateral sclerosis
by: Esther Álvarez-Sánchez, et al.
Published: (2025-01-01)

Cell ontology in an age of data-driven cell classification
by: David Osumi-Sutherland
Published: (2017-12-01)

Spatial gene regulatory networks driving cell state transitions during human liver disease
by: Nigel L Hammond, et al.
Published: (2025-04-01)

Single-cell RNA sequencing to dissect the immunological network of liver fibrosis in Schistosoma japonicum-infected mice
by: Yu Zhang, et al.
Published: (2022-12-01)

Editorial: Community series in unveiling immunological mechanisms of periodontal diseases, volume II
by: Pedro Paulo Chaves de Souza, et al.
Published: (2025-02-01)

Whole organism profiling of the Timp gene family
by: David Peeney, et al.
Published: (2023-06-01)

Single cell cortical bone transcriptomics define novel osteolineage gene sets altered in chronic kidney disease
by: Rafiou Agoro, et al.
Published: (2023-01-01)

Editorial: Unravelling human placental (patho-) physiology at the epigenetic and transcriptome level
by: Athina Samara, et al.
Published: (2023-06-01)

Comparing gene-gene co-expression network approaches for the analysis of cell differentiation and specification on scRNAseq data
by: Alisa Pavel, et al.
Published: (2025-01-01)

Editorial: Autoantibodies and the role of RNA/RNA therapy in rheumatoid arthritis
by: Kongyang Ma
Published: (2022-10-01)

A mini-review on perturbation modelling across single-cell omic modalities
by: George I. Gavriilidis, et al.
Published: (2024-12-01)

Differential detection workflows for multi-sample single-cell RNA-seq data
by: Jeroen Gilis, et al.
Published: (2025-10-01)

The First Transcriptomic Atlas of the Adult Lacrimal Gland Reveals Epithelial Complexity and Identifies Novel Progenitor Cells in Mice
by: Vanessa Delcroix, et al.
Published: (2023-05-01)

Spatiotemporal analysis of lung immune dynamics in lethal Coccidioides posadasii infection
by: Oscar A. Davalos, et al.
Published: (2025-05-01)

Single-cell RNAseq identifies clonally expanded antigen-specific T-cells following intradermal injection of gold nanoparticles loaded with diabetes autoantigen in humans
by: Stephanie J. Hanna, et al.
Published: (2023-10-01)

Multi-Omics Integration with Machine Learning and Molecular Docking Reveals Crosstalk Mechanisms and Drug Candidates in Metastatic Melanoma and Vitiligo
by: Yang H, et al.
Published: (2025-08-01)

Single-cell and bulk RNAseq unveils the immune infiltration landscape and targeted therapeutic biomarkers of psoriasis
by: Wenhui Deng, et al.
Published: (2024-04-01)