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eSPRESSO

31-Mar-2022: espresso 1.0.1 released.


espresso is a package for domain estimation of cells only from gene expression profile based on graph-structured stochastic self-organizing map (graph-SOM) and Markov chain Monte Carlo (MCMC) method.

Installation

Download a code espresso-X.X.X.tar.gz or espresso-X.X.X.zip from this repository, and install by the following command.

install.packages("espresso-X.X.X.tar.gz", repos = NULL, type = "source")

As an alternative way, espresso can be installed directly from GitHub.

library(devtools)
install_github("tmorikuicr/espresso")

Usage

Refer to the following documentation for the usage of espresso package.
31-Mar-2022: Vignette

Data availability

Gene expression data can be downloaded from the following link:
04-Apr-2022: espresso data

Citing

To cite your use of the espresso software, please reference the following paper:

  • Tomoya Mori, Toshiro Takase, Kuan-Chun Lan, Junko Yamane, Cantas Alev, Kenji Osafune, Jun Yamashita, and Wataru Fujibuchi. eSPRESSO: a spatial self-organizing-map clustering method for single-cell transcriptomes of various tissue structure using graph-based networks. bioRxiv. doi: http://doi.org/10.1101/2020.12.31.424948.