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immunedeconv 사용법

immunedeconv 사용법

Documentation

Getting started with immunedeconv
Methods like fluorescence activated cell sorting (FACS) or Immunohistochemistry (IHC)-staining have been used as a gold standard to estimate the immune cell content within a sample, however these methods are limited in their scalability and by the availability of good antibodies against the cell type markers.
https://icbi-lab.github.io/immunedeconv/articles/immunedeconv.html

설치

conda create -n deconvolution conda activate deconvolution conda install -c bioconda -c conda-forge r-immunedeconv
Shell
복사

Method는 크게 2가지로 구분된다.

Marker gene-based: MCP-counter, xCell
Deconvolution: CIBERSORT, quanTIseq, EPIC, TIMER

Input은 gene x sample matrix

•
TPM-normalized 되어 있어야 하고
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log-transformation은 하지 말아야 한다.
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Rowname 들은 HGNC gene symbol 들이어야 한다.

실행

immunedeconv::deconvolute(gene_expression_matrix, method)
Shell
복사
gep = read.csv('/data2/project/dohoon/mecon/data/TCGA-EXP/tpms_per_cancer_types/LAML.csv', row.names=1)
Shell
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method 종류

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quantiseq
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timer
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cibersort
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cibersort_abs
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mcp_counter
•
xcell
•
epic