CDSeq-R-package: CDSeq: A package for complete deconvolution using sequencing data
Description
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.
Arguments
Reduce-Recover
CDSeq uses reduce-recovery strategy and CPU parallel computing to speed up the deconvolution.
Hyperparameter estimation
Estimate hyperparameter for cell-type-specific GEPs (i.e. beta) using reference profile when cell_type_number is scalar.
Estimating number of cell type
Estimate number of cell types when cell_type_number is a vector of integers.
Partition on input bulk RNA-seq data
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.