The R package ‘contamDE’ conducts differential expression (DE) analysis using high throughput next-generation RNA-seq read count data generated from contaminated tumor samples that are either matched or unmatched with normal samples, which estimates the proportion of pure tumor cells in each contaminated tumor sample, and provides tumor vs.
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contamDE: Differential expression analysis of RNA-seq data for contaminated tumor samples.
Shen Q, Hu J, Jiang N, Hu X, Luo Z, Zhang H.
Bioinformatics. 2015 Nov 9. pii: btv657.