Browsers
Researchers at UC Santa Cruz were the first to assemble the human genome sequence, publish it on the web, and create a human genome browser, which evolved into what is now known as the UCSC Genome Browser. It is now an essential tool in biomedical science.
UCSC Genome Browser
For more than 20 years, the UCSC Genome Browser has been a free resource providing genomic scientists with graphical tools to display genome sequences. This interactive web-based “microscope” allows researchers to view all 23 chromosomes of the human genome at any scale, from a full chromosome to an individual nucleotide. It receives over a million hits daily and has become an essential tool for genomic researchers.
UCSC SARS-CoV-2 Genome Browser
A one-stop shop for COVID-19 research, the UCSC SARS-CoV-2 Genome Browser (“the virus browser”) is built on the strength of the UCSC Genome Browser to display the genome sequencing of thousands of viral samples, helping researchers study mechanisms of infection, transmission, mutation and variation, as well as the response of the human immune system.
Xena
UCSC Xena is a bioinformatics tool which visualizes functional genomics data from multiple sources all at once, including public and private data.
UCSC Cell Browser
Single-cell analysis is the current hot topic in genomics right now. This is because new droplet-based machines have brought single-cell gene expression assays into the < $1000 range, bringing them within reach of most research groups. Genomic analysis generally creates too many data points to show everything in a single image: For example, if you sequence 100.000 cells and the machines measure 20,000 genes per cell, the resulting data table has billions of values.
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It’s impossible for a human to get much out of such a table without some tool to help them. Researchers need interactive solutions to help them visualize the data and share it with others via the web. The UCSC Cell Browser, created by the UCSC Genome Browser team, is one of the solutions being developed right now to address this challenge. The UCSC Cell Browser works like a map viewer, but it plots circles instead of landscapes. Every circle represents a cell. Users can color the circles to designate gene expression; usually brighter values mean higher expression of a gene. You can also color-code according to annotations added manually by researchers, like patient age or body part of the cell. We are working to enhance the UCSC Cell Browser, improving the annotation interface and interactivity.
UCSC Ebola Virus Genome Browser
The 2014 Ebola epidemic in West Africa has stirred international response, renewing efforts to develop compelling preventative and treatment options. In response to requests for help from vaccine researchers, we have fast-tracked the UCSC Ebola Genome Browser. The browser is built with viral sequences from previous outbreaks, including the 2014 outbreak. This site also provides related tools and information which can be used to further the understanding of Ebola.