Announcing ONTraC

We are excited to present ONTraC . This is a new method for analyzing spatial omics data, focusing on reconstructing spatial niche trajectories. The software is available at GitHub. Excellent work by Wen, Shiwei, and Crystal!

Giotto Suite released

We are proud to release Giotto Suite after several years’ preparation. Giotto Suite greatly extends the functionality, flexibility, scalability, and interoperability compared to the original Giotto package. It implements a completely new design of the core data framework allowing technology-agnostic, multi-scale spatial multi-omic data analysis. This has been a great collaboration with Ruben Dries’ lab at Boston University. Many thanks to Jiaji (George) Chen, Joselyn Chavez, and the entire Giotto team!

New NIH grant awarded

We have received a new NIH RF1 grant to develop computational tools to facilitate harmonizing spatial transcriptomics data and integrating with additional data types for the BRAIN Initiative. We are recruiting a new postdoc to join in this effort.

DWLS is now on CRAN

DWLS is a cell-type deconvolution method previously developed by Daphne Tsoucas from our lab. To make this tool readily accessible to the broad community,  we have now converted it to a CRAN package which can be located here. Great work by Adriana!

Joining in BICCN

We have received a new RF1 grant to create a regulome and transcriptome atlas of fetal and adult human neurogenesis in collaboration with Profs. Roussos, Cai, and Hof labs. We are excited to join in the NIH BICCN network and look forward to collaborating other investigators in the consortium.

Giotto paper published

Our Giotto paper has been published in Genome Biology. Giotto is a comprehensive and open-source software package for spatial data analysis and visualization. It contains many functionalities such as cell-type identification, deconvolution, spatial pattern detection, cell neighborhood analysis, ligand-receptor detection, and interactive visualization.  We welcome users to check out our project and GitHub websites.