We blog about genomics. We also make a platform for open-source analysis of next generation data in the cloud. Hello.

Highly Customizable Multi-sample Single Cell RNA-Seq Pipeline on the CGC

“To study human biology, we must know our cells!”  – this is a quote from a paper published a couple of years back [1], where authors of the paper presented early-stage ideas and proofs-of-concept behind The Human Cell Atlas Project, an international collaborative effort aiming to define all human cell …

Written by Nevena Vukojičić, Aleksandar Daničić, Cera Fisher

Meeting the NIH Data Management and Sharing (DMS) policy requirements with community-focused cloud platforms

The Velsera suite of NIH-funded platforms including Cancer Genomics Cloud (CGC), BioData Catalyst Powered by Seven Bridges (BDC-Seven Bridges) and CAVATICA provide secure, interoperable and scalable biomedical data analysis solutions for governments, universities, institutions, and research consortia. The platforms enable a shared research environment that empower the users to bring …

Written by Surya Saha, Michele Mattioni, Jared Rozowsky, Zélia Worman

Manifest-based DRS import: A practical solution for cross-dataset analysis to empower translational research

A key challenge in data discovery is the coordination and assembly of datasets spanning multiple from across Data Coordination Centers on a cloud compute platform in a way that is both easy to use and meaningful. To meet this challenge, we have implemented a GA4GH Data Repository Service (DRS) manifest-based …

Written by Surya Saha

Visualizing multiomics data with the OmicCircos app on CGC

Seven Bridges (Velsera) is excited to announce the launch of the OmicCircos R shiny app on the Cancer Genomics Cloud (CGC) platform. The OmicCircos app has been developed in collaboration with the Dr. Daoud Meerzaman laboratory at the NCI, developers of the R Bioconductor OmicCircos package. The R shiny application …

Written by Divya Sain

Looking for an interactive variant association visualizer that produces publication quality plots?

GWAS results can be difficult to interpret, especially for those without a scripting background. Genome Wide Association Studies (GWAS) has revealed loci associated with common human genetic diseases such as coronary artery disease in genetically diverse populations.Single variant association tests are used in testing for association between genetic variants and …

Written by Aarthi Krishnan

We are excited to announce the release of dbGaP Submission Form Suite!

This is a new RShiny App on the Cancer Genomics Cloud (CGC) that streamlines the way a CGC user can submit their data to dbGAP! The dbGaP Submission Form Suite app allows a user to easily import, map and prepare their data for import into the database of Genotypes and …

Written by Biran Lassiter

The Cancer Genomics Cloud: Connecting Scientists Across the Globe

The 2nd DSI Africa Consortium Meeting kicked off on October 29th, 2022! This exciting conference brought together over 200 scientists and stakeholders from across Africa, and internationally. There, they exchanged ideas and showcased their work in Data Science and health. One of the scientists in attendance was Judy Wawira Gichoya, …

Written by Rowan Beck, PhD -- Community Engagement Manager

Machine Learning and Image Processing on the CGC: Tools For Success

Machine learning is becoming ubiquitous in the bioinformatics space: applying machine learning algorithms to analysis of proteomics, genomics, and other -omics datasets has provided a wealth of analysis and interpretations of data not easily achievable by conventional methods. The CGC offers many helpful features for users performing machine learning (ML) …

Written by Dan Ventre PhD, Soner Koc, and Ana Stankovic

Multi-Omics Analysis on the CGC: Applications in Epigenetics Research

The growing diversity of large cancer datasets has led to increased capabilities for multi-omics research. Multi-omics analysis is a promising approach to reveal the functionality of complex biological systems and processes. However, multi-omics analysis is a complex process that needs to be carefully designed and conducted, beginning from sampling all …

Written by Daniel Ventre PhD, Vesna Pajic PhD, and Jeffrey Grover PhD

We are always engaged in research and development, working to build the future of genomics, science, and health. Let's work together. We'd love to hear about your projects and challenges, so drop us a line. get in touch