Package index • multideconv

Main

Compute cell type deconvolution

compute.deconvolution(): Compute deconvolution
compute.deconvolution.analysis(): Compute cell type processing
deconvolution_dictionary(): Build a Deconvolution–Pathway Relationship Dictionary
compute.deconvolution.preprocessing(): Compute deconvolution preprocessing
compute_methods_variable_signature(): Compute deconvolution methods with variable signatures
replicate_deconvolution_subgroups(): Replicate deconvolution subgroups in a new dataset
prepare_multideconv_folds(): Prepare folds for multideconv cross-validation with processed training and test data

Single cell data manipulation for deconvolution

create_metacells(): Create meta-cells from a single cell object using the KNN algorithm. This function is adapted from the R package hdWGCNA (Morabito et al., 2023)
create_sc_pseudobulk(): Create pseudo bulk from single cell object
create_sc_signatures(): Create cell type signatures from scRNAseq
compute_sc_deconvolution_methods(): Compute second-generation deconvolution methods
compute.benchmark(): Compute deconvolution benchmark

Internal use (not exported functions)

computeCBSX(): Computes CIBERSORTx (CBSX) using one signature
computeCBSX_parallel(): Compute CIBERSORTx (CBSX) in parallel across multiple signatures
computeDWLS(): Computes DWLS
computeDWLS_parallel(): Compute DWLS in parallel across multiple signatures
computeDeconRNASeq(): Computes DeconRNASeq
computeEpiDISH(): Computes EpiDISH
computeMCP(): Computes MCPcounter
computeMOMF(): Computes MOMF
computeMOMF_parallel(): Compute MOMF in parallel across multiple signatures
computeQuantiseq(): Computes QuanTIseq
computeXCell(): Computes XCell
compute_subgroups(): Compute deconvolution subgroups
compute.cell.types(): Cell types split from deconvolution
remove_subgroups(): Remove subgroups that have the same method across different signatures
remove_low_variance(): Remove low variance deconvolution features
find.maximum.iteration(): Find maximum iteration from subgroups
removeCorrelatedFeatures(): Remove high correlated cell deconvolution features
correlation(): Perform pairwise correlation across all features

Example data