The R package ‘contamDE’ conducts differential expression (DE) analysis using high throughput next-generation RNA-seq read count data generated from contaminated tumor samples and normal samples. Two methods are implemented in this R package, one is contamDE (Shen et al., 2016) and the other is contamDE-lm (Ji et al., 2019).
Installation of the R package ‘contamDE’ in R:
devtools::install_github('zhanghustc/contamDE');
SHEN Qi, HU Jiyuan, JIANG Ning, HU Xiaohua, LUO Zewei, and ZHANG Hong (2016) contamDE: Differential expression analysis of RNA-seq data for contaminated tumor samples. Bioinformatics 32(5): 705-712.
JI Yifan, YU Chang, and ZHANG Hong (2019) contamDE-lm: Linear model based differential gene expression analysis using next generation RNA-seq data from contaminated tumor samples.