Nathan C. Sheffield

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 13

Top Topics

Biological Entities

Top Venues

Nucleic Acids Res.

J. Open Source Softw.

Publications

Guangzhi Xiong, Nathan Leroy, Stefan Bekiranov, Nathan C. Sheffield, Aidong Zhang
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. Bioinform. 40 (7) (2024)
Jonathan D. Ogata, Wancen Mu, Eric S. Davis, Bingjie Xue, J. Chuck Harrell, Nathan C. Sheffield, Douglas H. Phanstiel, Michael I. Love, Mikhail G. Dozmorov
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies. Bioinform. 39 (4) (2023)
Oleksandr Khoroshevskyi, Nathan Leroy, Vincent P. Reuter, Nathan C. Sheffield
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA. Bioinform. 39 (3) (2023)
Erfaneh Gharavi, Aaron Gu, Guangtao Zheng, Jason P. Smith, Hyun Jae Cho, Aidong Zhang, Donald E. Brown, Nathan C. Sheffield
Embeddings of genomic region sets capture rich biological associations in lower dimensions. Bioinform. 37 (23) (2021)
Jianglin Feng, Nathan C. Sheffield
IGD: high-performance search for large-scale genomic interval datasets. Bioinform. 37 (1) (2021)
Andrew D. Yates, Jeremy Adams, Somesh Chaturvedi, Robert Davies, Matthew R. Laird, Rasko Leinonen, Rishi Nag, Nathan C. Sheffield, Oliver Hofmann, Thomas M. Keane
Refget: standardized access to reference sequences. Bioinform. 38 (1) (2021)
Jianglin Feng, Aakrosh Ratan, Nathan C. Sheffield
Augmented Interval List: a novel data structure for efficient genomic interval search. Bioinform. 35 (23) (2019)
V. P. Nagraj, Neal E. Magee, Nathan C. Sheffield
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Nathan C. Sheffield, V. P. Nagraj, Vince Reuter
simpleCache: R caching for reproducible, distributed, large-scale projects. J. Open Source Softw. 3 (21) (2018)
Zhenjia Wang, Mete Civelek, Clint L. Miller, Nathan C. Sheffield, Michael J. Guertin, Chongzhi Zang
BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. Bioinform. 34 (16) (2018)
John T. Lawson, Eleni M. Tomazou, Christoph Bock, Nathan C. Sheffield
MIRA: an R package for DNA methylation-based inference of regulatory activity. Bioinform. 34 (15) (2018)
Boris Simovski, Chakravarthi Kanduri, Sveinung Gundersen, Dmytro Titov, Diana Domanska, Christoph Bock, Lara Bossini-Castillo, Maria Chikina, Alexander V. Favorov, Ryan M. Layer, Andrey A. Mironov, Aaron R. Quinlan, Nathan C. Sheffield, Gosia Trynka, Geir Kjetil Sandve
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Nathan C. Sheffield, Christoph Bock
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. Bioinform. 32 (4) (2016)