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


< Back to DB search