Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

11.7K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.7K
Ribosome Profiling02:24

Ribosome Profiling

4.0K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Early neutrophil infiltration promotes TRIMELVax-induced antitumor immunity by linking local inflammation to tumor control.

Oncoimmunology·2026
Same author

Improving Gallbladder Cancer Outcomes with Antibody-Based Therapies and Immunological Profiling: A Literature Review.

Antibodies (Basel, Switzerland)·2026
Same author

GRNContext: An Interactive Web Platform for Contextualized Gene Regulatory Networks Visualization Across Human Cancers.

Bioinformatics (Oxford, England)·2026
Same author

Phase I trial of a heat-conditioned tumor lysate vaccine (TRIMELVax) in anti-PD-1 refractory melanoma: safety and immunological aspects (NCT06556004).

British journal of cancer·2026
Same author

Lymphodepleting preconditioning impairs host antitumor immunity induced by adoptive T cell therapy in mouse models.

Nature communications·2026
Same author

Contrasting functions of CD73 and adenosine in CD8+ T-cell exhaustion during antitumor immunity.

Oncoimmunology·2026

Related Experiment Video

Updated: Jan 10, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

19.0K

scExplorer: a comprehensive web server for single-cell RNA sequencing data analysis.

Sergio Hernández-Galaz1,2,3, Andrés Hernández-Olivera2, Felipe Villanelo4

  • 1Laboratorio de Redes Biológicas, Fundación Ciencia and Vida, Huechuraba, Santiago, 8580702, Chile.

Bioinformatics Advances
|November 21, 2025
PubMed
Summary
This summary is machine-generated.

scExplorer is a web platform simplifying single-cell RNA sequencing (scRNA-seq) analysis for non-programmers. It offers advanced batch correction, scalable job management, and reproducible reporting for complex datasets.

More Related Videos

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

321
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response
09:45

Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response

Published on: August 10, 2017

8.6K

Related Experiment Videos

Last Updated: Jan 10, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

19.0K
Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

321
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response
09:45

Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response

Published on: August 10, 2017

8.6K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Single-cell RNA sequencing (scRNA-seq) analysis requires specialized computational skills, posing a barrier for many researchers.
  • Integrating multiple scRNA-seq datasets, managing large-scale computations, and ensuring workflow reproducibility are significant challenges.

Purpose of the Study:

  • To develop a user-friendly, web-based platform, scExplorer, to overcome computational barriers in scRNA-seq data analysis.
  • To provide researchers, especially those without programming expertise, with tools for comprehensive and reproducible scRNA-seq analysis.

Main Methods:

  • Implemented comprehensive batch correction using four algorithms: ComBat, Scanorama, BBKNN, and Harmony.
  • Integrated SLURM-based job scheduling with pause/resume capabilities for efficient, large-scale analysis.
  • Developed automated generation of publication-ready reports with exportable configuration files for full reproducibility.

Main Results:

  • scExplorer successfully integrates multiple state-of-the-art batch correction algorithms.
  • The platform supports scalable job management for datasets up to hundreds of thousands of cells.
  • Automated reporting and configuration file export ensure transparency and reproducibility.

Conclusions:

  • scExplorer democratizes scRNA-seq analysis by removing technical hurdles for non-computational researchers.
  • The platform enhances collaborative research by providing transparent, reproducible, and accessible tools for complex data analysis.