mMCP-counter

Murine version of MCP-counter, a tool to estimate the immune and stromal composition of heterogeneous tissue, from transcriptomic data. It is distributed as a R package.

Installation

In a R session, install from the GitHub repository using devtools:

install.packages("devtools")
library(devtools)
devtools::install_github("cit-bioinfo/mMCP-counter")

Usage

The mMCP-counter package exports one function, mMCPcounter.estimate. To use it:

library("mMCPcounter")
mMCPcounter.estimate(expressionData, features = c("Gene.Symbol","ENSEMBL.ID","Probes")[1], genomeVersion = c("GCRm38","GCRm39")[2])

For more details, please refer to:

?mMCPcounter::mMCPcounter.estimate

Citation

If you use mMCP-counter in a scientific publication, please cite:

Petitprez, F., Lévy, S., Sun, C.-M., Meylan, M., Linhard, C., Becht, E., Elarouci, N., Tavel, D., Roumenina, L.T., Ayadi, M., Sautès-Fridman, C., Fridman, W.H. and de Reyniès, A. The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression. Genome Med 12, 86 (2020). https://doi.org/10.1186/s13073-020-00783-w

Acknowledgement

The authors thank Lorenzo Merotto for his help with the support of the new genome version GCRm39.

License

mMCP-counter is a free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.