scScope
scScope is a software tool that harnesses the power of large-scale single-cell RNA sequencing (scRNA-seq) data to determine and characterize cell types within heterogeneous tissues. At the core of scScope is a scalable deep-learning-based approach capable of processing millions of single-cell gene expression profiles efficiently. This capability is essential in the context of scRNA-seq, which generates vast amounts of data, allowing for the detailed examination of cellular heterogeneity at an unprecedented scale.
The primary innovation of scScope lies in its ability to accurately and rapidly identify the composition of cell types from the noisy and complex datasets typical of single-cell gene expression studies. Traditional methods of analyzing such data can be time-consuming and may not always effectively handle the inherent noise and variability of single-cell measurements. scScope, however, employs advanced deep learning techniques adept at recognizing patterns and distinguishing between different cellular states, even in the presence of significant noise.
Topic
RNA-seq;Transcriptomics;Genotype and phenotype
Detail
Operation: Imputation;Splitting;Expression analysis
Software interface: Library
Language: Python
License: Apache License, Version 2.0
Cost: Free with restrictions
Version name: -
Credit: The National Institutes of Health (NIH).
Input: -
Output: -
Contact: Lani F. Wu lani.wu@ucsf.edu, Steven J. Altschuler steven.altschuler@ucsf.edu
Collection: -
Maturity: Stable
Publications
- Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning.
- Deng Y, et al. Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning. Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning. 2019; 16:311-314. doi: 10.1038/s41592-019-0353-7
- https://doi.org/10.1038/s41592-019-0353-7
- PMID: 30886411
- PMC: PMC6774994
Download and documentation
Documentation: https://github.com/AltschulerWu-Lab/scScope/blob/master/README.md
Home page: https://github.com/AltschulerWu-Lab/scScope
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