InfiniumPurify: Estimate and Account for Tumor Purity in Cancer Methylation Analysis
The proportion of cancer cells in solid tumor sample, known as the tumor purity, has adverse impact on a variety of data analyses
if not properly accounted for. We develop 'InfiniumPurify', which is a comprehensive R package for estimating and accounting for
tumor purity based on DNA methylation Infinium 450k array data. 'InfiniumPurify' provides functionalities for tumor purity
estimation. In addition, it can perform differential methylation detection and tumor sample clustering with the consideration
of tumor purities.
PREDE: Deconvolution of heterogeneous tumor samples using partial reference signals
Deconvolution of heterogeneous bulk tumor samples into distinct cell populations is an important yet challenging problem,
particularly when only partial references are available. Here we developed PREDE, a partial reference deconvolution method based on iterative non-negative Matrix
Factorization.
Purimeth: an integrated web server for tumor purity estimation and downstream analyses from DNA methylation array data
Proportion of non-cancerous cells in a tumor sample is an important indicator for the response of immunotherapies and also has a strong influence on multiple types of data analyses.
Here, we propose Purimeth, an integrated web server for estimating and accounting for tumor purity in cancer DNA methylation research. Purimeth implements three important methods for
tumor purity estimation from DNA methylation array data, i.e., InfiniumPurify, MEpurity and PAMES. Based on the tumor purity estimate, users are allowed to perform multiple downstream
analyses including differential methylation (DM), clustering and purification of tumor samples accounting for tumor purities.
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