SHARP
"SHARP" is a scalable tool for processing and clustering large-scale single-cell RNA-sequencing (scRNA-seq) data. Developed to address the challenges of dimension reduction and data analysis in massive scRNA-seq datasets without compromising data integrity, SHARP employs an ensemble random projection-based algorithm capable of handling datasets with up to 10 million cells.
Key Features and Functionalities:
Scalable Clustering: SHARP is specifically tailored for clustering very large scRNA-seq datasets, demonstrating scalability of up to 10 million cells. This feature makes it a valuable tool for analyzing data from extensive single-cell studies.
- Ensemble Random Projection-Based Algorithm: The core of SHARP's efficiency lies in its use of an ensemble random projection-based algorithm, which effectively reduces data dimensionality while preserving the essential structure required for accurate clustering.
Topic
RNA-Seq;Cell biology;Transcriptomics;Machine learning
Detail
Operation: Dimensionality reduction;Clustering;Essential dynamics
Software interface: Command-line interface
Language: R
License: GNU General Public License v3.0
Cost: Free with restrictions
Version name: 1.1.0
Credit: The National Institutes of Health (National Institute of Diabetes and Digestive and Kidney Diseases), the Novo Nordisk Foundation, Lundbeck Foundation.
Input: -
Output: -
Contact: Kyoung Jae Won kyoung.won@bric.ku.dk
Collection: -
Maturity: -
Publications
- SHARP: Single-cell RNA-seq Hyper-fast and Accurate Processing via Ensemble Random Projection
- Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
- https://doi.org/10.1101/461640
- PMID: -
- PMC: -
- SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projection.
- Wan S, et al. SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projection. SHARP: hyperfast and accurate processing of single-cell RNA-seq data via ensemble random projection. 2020; 30:205-213. doi: 10.1101/gr.254557.119
- https://doi.org/10.1101/GR.254557.119
- PMID: 31992615
- PMC: PMC7050522
Download and documentation
Source: https://github.com/shibiaowan/SHARP/releases/tag/1.1.0
Documentation: https://github.com/shibiaowan/SHARP/blob/master/README.md
Home page: https://github.com/shibiaowan/SHARP
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