CDSeq Evaluation
The CDSeq R package can be found below. https://github.com/kkang7/CDSeq_R_Package
Using the the deconvolution benchmark established by Francisco Avila Cobos, et al (https://github.com/favilaco/deconv_benchmark), we simulate the data for deconvolution using the single cell data from
(1) PBMC dataset (Ding, Jiarui, et al. "Systematic comparison of single-cell and single-nucleus RNA-sequencing methods." Nature biotechnology (2020): 1-10.)
(2) AD dataset (Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature. 2019 May 1:1)
(3) Tumor dataset(Puram, Sidharth V., et al. "Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer." Cell 171.7 (2017): 1611-1624.).