Description Reduce-Recover Hyperparameter estimation Estimating number of cell type Partition on input bulk RNA-seq data Author(s) References
CDSeq-R-package
takes bulk RNA-seq data as input and simultaneously returns estimates of both cell-type-specific gene expression profiles and sample-specific cell-type proportions.
CDSeq uses reduce-recovery strategy and CPU parallel computing to speed up the deconvolution.
Estimate hyperparameter for cell-type-specific GEPs (i.e. beta) using reference profile when cell_type_number is scalar.
Estimate number of cell types when cell_type_number is a vector of integers.
When block_number (number of partition on the bulk RNASeq data) is 1, whole bulk_data will be used. GEP is not from reduce-recovery.
Kai Kang, David Huang, kangkai0714@gmail.com
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007510
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