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https://github.com/ebecht/MCPcounter

Last synced: 17 days ago
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Host: GitHub
URL: https://github.com/ebecht/MCPcounter
Owner: ebecht
Created: 2016-09-08T10:37:58.000Z (almost 8 years ago)
Default Branch: master
Last Pushed: 2022-06-21T14:51:01.000Z (about 2 years ago)
Last Synced: 2024-02-28T20:37:11.100Z (4 months ago)
Language: R
Size: 98.6 KB
Stars: 52
Watchers: 6
Forks: 42
Open Issues: 6
Metadata Files:
- Readme: README.md

Lists

awesome-deconvolution - MCPcounter - counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data (see also: [Becht et al 2016](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1070-5)); tags: immune; immune_cell; blood; blood_cell; transcriptomics; microenvironment; human (Methods)

README

        # MCPcounter

This repository hosts the source code corresponding to the method described in our 2016 paper published in Genome Biology, [Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1070-5)

To install it, the easiest is to use the `R` package `devtools` and its function `install_github`. To do so, open an `R` session and enter

    install.packages(c("devtools","curl")) ##Installs devtools and the MCPcounter dependancy 'curl'

    library(devtools)

    install_github("ebecht/MCPcounter",ref="master", subdir="Source")

    

Examples on how to run the algorithm on your data are shown in the documentation `?MCPcounter.estimate`