Author

Raymond G. Cavalcante

University of MichiganORCID 0000-0002-6986-4283Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Research Focus:benchmarking· 2 Assay:ChIP-seq· 2 Assay:DNA methylation· 2 Organism:human· 2 Approach:benchmark study· 1 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Maureen A. SartoriD· 3 shared Alan P. BoyleiD· 2 shared Shuze WangiD· 2 shared Snehal B. PatiliD· 2 shared Tingting QiniD· 2 shared Agata MuszyńskaiD· 1 shared Alexander BlumeiD· 1 shared Alicia AlonsoiD· 1 shared

Activity by Year

2017-2020 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersBioinformatics

Maureen A. SartorORCID

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Author profile →

4 papers

Recent·Most cited

The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle R. Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond G. Cavalcante, Anders Lundmark, Daniel Butler, Chris Mozsary, Justin Gurvitch, , Christopher E. Mason

The paper evaluates epigenetic methods using reference materials, finding high concordance between assays and differences in performance across platforms.

bioRxiv · Dec 14, 2020 · PreprintGenomics

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

Tingting Qin, Christopher Lee, Raymond G. Cavalcante, Peter Orchard, Heming Yao, Hanrui Zhang, Shuze Wang, Snehal B. Patil, Alan P. Boyle, Maureen A. Sartor

The paper develops genome-wide enhancer-to-target gene assignments across >500 cell types and shows they outperform naive methods in gene set enrichment analysis.

bioRxiv · Oct 22, 2020 · PreprintBioinformatics

Poly-Enrich: Count-based Methods for Gene Set Enrichment Testing with Genomic Regions

Christopher Tai-Yi Lee, Raymond G. Cavalcante, Chee Khoon Lee, Tingting Qin, Snehal B. Patil, Shuze Wang, Zing Tsung‐Yeh Tsai, Alan P. Boyle, Maureen A. Sartor

Poly-Enrich improves gene set enrichment testing for genomic regions by modeling peak counts with a negative binomial model, outperforming previous methods in certain scenarios.

NAR Genomics and Bioinformatics · Feb 6, 2020Peer-reviewedBioinformatics

annotatr: Genomic regions in context

Raymond G. Cavalcante, Maureen A. Sartor

annotatr summarizes and visualizes genomic region annotations, offering faster and more flexible analysis than existing tools.

Bioinformatics · Mar 28, 2017Peer-reviewedBioinformatics