mMCP-counter
mMCP-counterは、特定の条件に基づいてカウントを自動化するツールです。ユーザーは簡単に設定を行い、リアルタイムでデータを追跡できます。使いやすいインターフェースと多機能性を兼ね備えており、業務の効率化に寄与します。
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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/.