cell.proportions |
Cell Proportion data Example cell proportions of circulating immune cell subpopulations from 5 healthy individuals |
count.table |
Expression data Example RNA-seq data from 5 healthy individuals |
dCell.evaluate |
Evaluate percentage of coeficient used in a model 'dCell.predict' Predicts cell proportions of 32 cell subpopulations usin decon Cell models. |
dCell.exp.trimming |
Trims a dCell.exp matrix for only dCell genes 'dCell.predict' Loads a the gene list used in all dCell models and trims a dCell.exp matrix. |
dCell.expProcessing |
Pre-process RNASeq based expression data. 'dCell.expProcessing' Performes a TMM normalization, log2(counts+1) and scaling. |
dCell.geneList |
DeconCell gene list Vector of gene names (ENSEMBL identifiers) used in all of the Decon cell models |
dCell.models |
DeconCell models Lists fo 33 lists containing the coefficients used in the prediction of cell proportions using expression values |
dCell.names |
Cell subpopulation names Code and names for the predicted cell subpopulations in the DeconCell package |
dCell.predict |
Predict all available cell subpopoulation in DeconCell 'dCell.predict' Runs dCell.predict |
dCell.predict.single |
Predict a single cell subpopoulation using a DeconCell model 'dCell.predict.single' Predicts cell proportions of one out of the 32 cell subpopulations using the DeconCell models. |
dCell.run |
Run Decon-cell to generate new gene signature and characterize marker genes. 'dCell.run' Runs dCell.run to generate gene expression signatures to predict cell proportions of bulk tissues |
dCell.run.single |
Run DeconCell to generate new gene signature for a single cell type. 'dCell.run.single' Runs dCell.run to generate gene expression signatures to predict cell proportions of bulk tissues |
get.marker.genes |
Wrapper function for glmnet 'get.marker.genes' |
glmnet.wrapper |
Wrapper function for glmnet 'glmnet.wrapper' |