Software
Our Computational Tools
We develop open-source software for genomic data analysis, with a focus on cancer research and single-cell methods.
Corral
Single-cell RNA-seq dimension reduction, batch integration, and visualization with correspondence analysis.
Publications
MOGSA
Multi-Omics Gene Set Analysis: Integrative analysis of multiple experimental and molecular data types.
Publications
iBBiG
Iterative Binary Bi-clustering of Gene Sets for biclustering and pattern discovery in gene expression data.
Publications
made4
Multivariate Analysis of Microarray Data using ADE4 for visualization and analysis of microarray data.
Publications
Workshops & Training Materials
Hitchhiker’s Guide to PCA
A comprehensive tutorial on Principal Component Analysis for genomic data.
Quick Guide to scRNAseq
Introduction to single-cell RNA sequencing analysis methods.
BIRSBiointegration Hackathon
Datasets and code from our multi-omics integration hackathon.
References
Culhane AC, Thioulouse J, Perriere G, Higgins DG. 2005. MADE4: an R package for multivariate analysis of gene expression data. Bioinformatics 21:2789–2790. doi:10.1093/bioinformatics/bti394
Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane AC. 2012. iBBiG: Iterative binary bi-clustering of gene sets. Bioinformatics (Oxford, England) 28:2484–92. doi:10.1093/bioinformatics/bts438
Hsu LL, Culhane AC. 2023. Correspondence analysis for dimension reduction, batch integration, and visualization of single-cell RNA-seq data. Scientific Reports 13. doi:10.1038/s41598-022-26434-1
Hsu LL, Culhane AC. 2020. Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data. Frontiers in Oncology 10:973. doi:10.3389/fonc.2020.00973
Lê Cao K-A, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, Singh A, Sodicoff JS, Stein-O’Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan G-C, Culhane AC, Fertig E. 2021. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biology 22. doi:10.1186/s13059-021-02433-9
Meng C, Basunia A, Peters B, Gholami AM, Kuster B, Culhane AC. 2019. MOGSA: Integrative Single Sample Gene-set Analysis of Multiple Omics Data. Molecular & Cellular Proteomics 18:S153–S168. doi:10.1074/mcp.tir118.001251
Meng C, Culhane A. 2016. Integrative exploratory analysis of two or more genomic datasets. Springer New York. pp. 19–38. doi:10.1007/978-1-4939-3578-9_2
Meng C, Kuster B, Culhane AC, Gholami AM. 2014. A multivariate approach to the integration of multi-omics datasets. BMC Bioinformatics 15. doi:10.1186/1471-2105-15-162
Meng C, Zeleznik OA, Thallinger GG, Kuster B, Gholami AM, Culhane AC. 2016. Dimension reduction techniques for the integrative analysis of multi-omics data. Briefings in Bioinformatics 17:628–641. doi:10.1093/bib/bbv108