schex

Schex is an R package to visualize single-cell RNA-sequencing (scRNA-seq) data, addressing challenges related to scale and sparsity. The tool utilizes hexagonal binning, offering advantages such as improved speed and reduced storage for resultant plots compared to traditional approaches.

Topic

RNA-Seq;Cell biology

Detail

  • Operation: Visualisation

  • Software interface: Command-line user interface

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.16.0

  • Credit: Sylvia and Charles Viertel Senior Medical Research Fellowship, Howard Hughes Medical Institute International Research Scholarship.

  • Input: -

  • Output: -

  • Contact: Saskia Freytag saskia.freytag@perkins.uwa.edu.au

  • Collection: -

  • Maturity: Stable

Publications

  • schex avoids overplotting for large single-cell RNA-sequencing datasets.
  • Freytag S and Lister R. schex avoids overplotting for large single-cell RNA-sequencing datasets. schex avoids overplotting for large single-cell RNA-sequencing datasets. 2020; 36:2291-2292. doi: 10.1093/bioinformatics/btz907
  • https://doi.org/10.1093/BIOINFORMATICS/BTZ907
  • PMID: 31794001
  • PMC: -

Download and documentation

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