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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
Flow Cytometry01:23

Flow Cytometry

The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
In...
DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Export of Mitochondrial and Chloroplast Genes02:19

Export of Mitochondrial and Chloroplast Genes

A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred irrespective...

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ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
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Published on: January 16, 2019

XVCF: Exquisite visualization of VCF data from genomic experiments.

Ghaida Almuneef1, Abdulrhman Aljouie2, Yahya Bokhari3

  • 1Artificial Intelligence and Bioinformatics Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.

SLAS Technology
|June 20, 2026
PubMed
Summary
This summary is machine-generated.

XVCF is a new R Shiny App that simplifies the visualization and summarization of genomic variation data. This user-friendly tool addresses challenges in interpreting large datasets, making genomic analysis more accessible.

Keywords:
ANNOVARCancer genomesGenomic analysisGraphical user interfaceShiny appSummarizationUser-friendlyVariant call format (VCF)Visualization

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing generates large genomic datasets, posing visualization and interpretation challenges.
  • Existing tools for visualizing genetic variants from VCF files often require command-line expertise, limiting accessibility.
  • There is a need for user-friendly, graphical tools to summarize and visualize genomic variation data.

Purpose of the Study:

  • To develop an interactive, GUI-based tool for summarizing and visualizing genomic variation data.
  • To provide an accessible solution for researchers facing challenges in interpreting large-scale genomic datasets.
  • To facilitate the analysis of both germline and cancer genomic data.

Main Methods:

  • Developed XVCF, an interactive Shiny App using the R programming language.
  • Utilized R packages 'vcfR' and 'maftools' for data visualization and quality control.
  • Implemented a graphical user interface (GUI) for interactive data loading, summarization, and visualization.

Main Results:

  • XVCF provides an easy-to-use interface for interactive genomic data summarization and visualization.
  • The tool extracts key information like read depth, mapping quality, genotype, and allele frequency.
  • XVCF analyzes cancer genomic data using 'maftools' to generate oncoplots, lollipop plots, and gene summaries.
  • XVCF is freely available on GitHub and compatible across different operating systems.

Conclusions:

  • XVCF offers a user-friendly solution for visualizing and summarizing genomic variation data.
  • The tool simplifies complex genomic data analysis through its intuitive GUI and powerful R Shiny framework.
  • XVCF enhances accessibility to genomic data interpretation for researchers lacking extensive programming knowledge.