Package index • multideconv

Main

Compute cell type deconvolution

compute.deconvolution(): Compute deconvolution

compute.deconvolution.analysis(): Compute cell type processing

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 functions

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

Utils

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

Package Data

Example data

raw_counts: Raw counts

deconv_bulk: Bulk deconvolution matrix

deconvolution: Deconvolution matrix

metacells_data: Metacells data

metacells_metadata: Metacells metadata

pseudobulk: Pseudobulk

cells_groundtruth: Cell groundtruth

subgroups: Cell subgroups

sample_labels: Sample labels

cell_labels: Cell labels