Algorithms and Methods for Integrative Analysis of Single Cell Omics Data
We are developing matrix factorization and clustering methods for the integrative analysis of scRNAseq and multi-omics single-cell data.
Corral
Corral is a method for single-cell RNA-seq dimension reduction, batch integration, and visualization using correspondence analysis.
Michael’s Demux
Michael’s Demux is a tool for demultiplexing single-cell sequencing data.
Software
Explore our software tools on the Software Page.
Publications
Funding Sources
This project is funded by the DoD and CZI Science Seed Network awards.
References
Gusenleitner, Daniel, Aedin Culhane, and Maintainer Aedin Culhane. n.d. “Package ‘iBBiG’.”
Hsu, Lauren L., and Aedin C. Culhane. 2020. “Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data.” Frontiers in Oncology 10: 973. https://doi.org/10.3389/fonc.2020.00973.
Hsu, Lauren L., and Aedín C. Culhane. 2021. “Corral: Single-Cell RNA-Seq Dimension Reduction, Batch Integration, and Visualization with Correspondence Analysis.” bioRxiv, January, 2021.11.24.469874. https://doi.org/10.1101/2021.11.24.469874.
Lê Cao, Kim-Anh, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, et al. 2021. “Community-Wide Hackathons to Identify Central Themes in Single-Cell Multi-Omics.” Genome Biology 22 (1): 220. https://doi.org/10.1186/s13059-021-02433-9.
Mirzayi, Chloe, Audrey Renson, Fatima Zohra, Shaimaa Elsafoury, Ludwig Geistlinger, Lora J. Kasselman, Kelly Eckenrode, et al. 2021. “Reporting Guidelines for Human Microbiome Research: The STORMS Checklist.” Nature Medicine 27 (11): 1885–92. https://doi.org/10.1038/s41591-021-01552-x.
Thorsson, Vésteinn, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, et al. 2018. “The Immune Landscape of Cancer.” Immunity 48 (4): 812–830.e14. https://doi.org/10.1016/j.immuni.2018.03.023.