【생물정보학】 CellPhoneDB Tutorial

CellPhoneDB Tutorial

 

추천글 : 【생물정보학】 리간드-수용체 상호작용 분석 

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1. 설치 [본문]

2. 레퍼런스 [본문]

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1. 설치 [목차]

⑴ 리눅스 환경 준비 혹은 anaconda3 설치 

⑵ 입력 파일

① cellphonedb_meta.txt

 

② cellphonedb_count.txt

 

 

⑶ 예제 코드  

 

# 1. 가상환경 생성 및 활성화
conda create -n cpdb python=3.7
activate cpdb # 혹은 conda activate cpdb
pip install cellphonedb
activate cpdb # 혹은 conda activate cpdb

# 2. 예시 데이터 설치
curl https://raw.githubusercontent.com/Teichlab/cellphonedb/master/in/example_data/test_counts.txt --output test_counts.txt
curl https://raw.githubusercontent.com/Teichlab/cellphonedb/master/in/example_data/test_meta.txt --output test_meta.txt

# 3. output 경로 설정 
mkdir custom_folder

# 4. cellphonedb 실행
cellphonedb method statistical_analysis cellphonedb_meta.txt cellphonedb_count.txt --output-path=custom_folder --counts-data=gene_name

 

① "--counts-data=gene_name"이 없으면 "All counts filtered: Are you using human data?" 에러 메시지가 출력됨

⑷ 생성 파일 

① deconvoluted.txt

② means.txt

③ pvalues.txt

④ values_means.txt

⑤ significant_means.txt

 

 

2. 레퍼런스 [목차]

⑴ https://pubmed.ncbi.nlm.nih.gov/32103204/

CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes - PubMed

⑵ https://www.cellphonedb.org/documentation

CellPhoneDB - Welcome

⑶ https://github.com/Teichlab/cellphonedb

 

GitHub - Teichlab/cellphonedb

 

입력: 2021.04.13 20:40