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Related Experiment Video

Updated: Sep 9, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

scafari: exploring scDNA-seq data.

Sophie-Marie Wind¹, Thea Reinkens², Yvonne Lisa Behrens³

¹Institute of Medical Informatics, University of Muenster, 48149 Muenster, Germany.

Bioinformatics (Oxford, England)

|September 2, 2025

Summary

This summary is machine-generated.

scafari is a new open-source tool for analyzing single-cell DNA sequencing data. It provides user-friendly quality control and variant analysis, addressing a gap in current bioinformatics software.

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Last Updated: Sep 9, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Published on: October 8, 2017

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Single-cell sequencing allows for individual cell expression pattern analysis.
Single-cell DNA sequencing provides insights into a single cell's genome.
Limited open-source software exists for processing and quality analysis of single-cell DNA sequencing data.

Purpose of the Study:

To introduce scafari, a novel open-source software tool.
To provide user-friendly data quality control for single-cell DNA sequencing.
To enable explorative variant analyses and visualization of single-cell DNA sequencing data.

Main Methods:

scafari is implemented as an R Bioconductor package.
The tool features an integrated shiny application for interactive use.
It is available for download at https://bioconductor.org/packages/scafari.

Main Results:

scafari offers easy-to-use data quality control.
The software facilitates explorative variant analyses.
Visualization of single-cell DNA sequencing data is supported.

Conclusions:

scafari addresses the need for user-friendly open-source software in single-cell DNA sequencing analysis.
The tool enhances the accessibility of quality control and variant analysis for this data type.
scafari empowers researchers to gain deeper insights from single-cell genome data.