| GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA O Khoroshevskyi, N LeRoy, VP Reuter, NC Sheffield Bioinformatics 39 (3), btad069, 2023 | 9 | 2023 |
| GenomicDistributions: fast analysis of genomic intervals with Bioconductor K Kupkova, JV Mosquera, JP Smith, M Stolarczyk, TL Danehy, JT Lawson, ... BMC genomics 23 (1), 299, 2022 | 5 | 2022 |
| Joint representation learning for retrieval and annotation of genomic interval sets E Gharavi, NJ LeRoy, G Zheng, A Zhang, DE Brown, NC Sheffield Bioengineering 11 (3), 263, 2024 | 3 | 2024 |
| Methods for evaluating unsupervised vector representations of genomic regions G Zheng, J Rymuza, E Gharavi, NJ LeRoy, A Zhang, NC Sheffield bioRxiv, 2023.08. 28.555137, 2023 | 3 | 2023 |
| Neuron activity dependent redox compartmentation revealed with a second generation red-shifted ratiometric sensor S Radhakrishnan, J Norley, S Wendt, N LeRoy, H Hall, S Norcross, ... ACS chemical neuroscience 11 (17), 2666-2678, 2020 | 3 | 2020 |
| Challenges to sharing sample metadata in computational genomics NC Sheffield, NJ LeRoy, O Khoroshevskyi Frontiers in Genetics 14, 1154198, 2023 | 2 | 2023 |
| Methods for constructing and evaluating consensus genomic interval sets J Rymuza, Y Sun, G Zheng, NJ LeRoy, M Murach, N Phan, A Zhang, ... bioRxiv, 2023.08. 03.551899, 2023 | 2 | 2023 |
| Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings NJ LeRoy, JP Smith, G Zheng, J Rymuza, E Gharavi, DE Brown, A Zhang, ... bioRxiv, 2023.08. 01.551452, 2023 | 2 | 2023 |
| Optipyzer: A fast and flexible multi-species codon optimization server N LeRoy, C Roleck bioRxiv, 2023.05. 22.541759, 2023 | 1 | 2023 |
| PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata NJ LeRoy, O Khoroshevskyi, A O'Brien, R Stepien, A Arslan, NC Sheffield bioRxiv, 2023.08. 15.551388, 2023 | | 2023 |
| DeepGSEA: Explainable Deep Gene Set Enrichment Analysis for Single-cell Transcriptomic Data G Xiong, NJ LeRoy, S Bekiranov, A Zhang bioRxiv, 2023.11. 03.565235, 2023 | | 2023 |
| FRET Biosensors: Engineering Fluorescent Proteins as Biological Tools for Studying Parkinson’s Disease NJ LeRoy, JR Norley, S Radhakrishnan, M Tantama | | 2017 |
