scRepertoire: TCR/BCR seq 분석하는 R package

📑 Borcherding, Nicholas, Nicholas L. Bormann, and Gloria Kraus. “scRepertoire: An R-based toolkit for single-cell immune receptor analysis.” F1000Research 9 (2020).

• 🔗 Bioconductor page
• 🔗 Github page
• 🔗 v1.10.1. Tutorial

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scRepertoire")

🚨 `ERROR: compilation failed for package ‘gsl’`

• 🔗 CRAN gsl page
• 🔗 GSL homepage
• 🔗 GSL download page

그냥 바로 R package 깔려고 하면 안깔림. C library부터 깔아줘야함.

GSL C library 설치

wget https://gnu.mirror.constant.com/gsl/gsl-latest.tar.gz
tar -xvzf gsl-latest.tar.gz
cd gsl-2.7.1/
./configure --prefix=/source/gsl-2.7.1
make -j 10 & make install
echo -e "PATH=/source/gsl-2.7.1/bin:$PATH" >> ~/.bash_profile  
echo -e "LD_LIBRARY_PATH=/source/gsl-2.7.1/lib:$LD_LIBRARY_PATH" >> ~/.bash_profile  
source ~/.bash_profile

다시 R로 돌아가서 gsl 설치.

install.packages("gsl")

How to run scRepertoire

Reference

• https://xuranw.github.io/MuSiC/articles/pages/MuSiC2.html#sample-analysis